Raspbian Package Auto-Building

Build log for bowtie2 (2.3.5.1-6) on armhf

bowtie22.3.5.1-6armhf → 2019-12-31 11:47:26

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02

+==============================================================================+
| bowtie2 2.3.5.1-6 (armhf)                    Tue, 31 Dec 2019 08:42:06 +0000 |
+==============================================================================+

Package: bowtie2
Version: 2.3.5.1-6
Source Version: 2.3.5.1-6
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-67f76782-ea37-429d-951b-2d50fc9b6622' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.2 MB in 10s (2523 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'bowtie2' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/bowtie2.git
Please use:
git clone https://salsa.debian.org/med-team/bowtie2.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 8855 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main bowtie2 2.3.5.1-6 (dsc) [2180 B]
Get:2 http://172.17.0.1/private bullseye-staging/main bowtie2 2.3.5.1-6 (tar) [8802 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main bowtie2 2.3.5.1-6 (diff) [50.5 kB]
Fetched 8855 kB in 2s (4202 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bowtie2-czQWnM/bowtie2-2.3.5.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bowtie2-czQWnM' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-5Oaw9y/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-5Oaw9y/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (10.0 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 29 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13002 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any all)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 12), help2man, libtbb-dev, python3, liblocal-lib-perl, libtest-deep-perl, libclone-perl, libfile-which-perl, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 12), help2man, libtbb-dev, python3, liblocal-lib-perl, libtest-deep-perl, libclone-perl, libfile-which-perl, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-bowtie2-dummy' in '/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive/sbuild-build-depends-bowtie2-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-bowtie2-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ Sources [553 B]
Get:5 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ Packages [634 B]
Fetched 2520 B in 0s (11.9 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install bowtie2 build dependencies (apt-based resolver)
-------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base help2man intltool-debian libarchive-zip-perl libbsd0
  libclone-perl libcroco3 libdebhelper-perl libelf1 libexpat1
  libfile-stripnondeterminism-perl libfile-which-perl libglib2.0-0 libicu63
  liblocal-lib-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libmodule-build-perl libmpdec2 libpipeline1 libpython3-stdlib
  libpython3.7-minimal libpython3.7-stdlib libsigsegv2 libssl1.1
  libsub-override-perl libtbb-dev libtbb2 libtest-deep-perl libtinfo5 libtool
  libuchardet0 libxml2 m4 man-db mime-support po-debconf python3
  python3-minimal python3.7 python3.7-minimal sensible-utils zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
  tbb-examples libtbb-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
  m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk
  python3-venv python3.7-venv python3.7-doc binfmt-support
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs libmodule-signature-perl libpod-readme-perl
  libsoftware-license-perl libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base help2man intltool-debian libarchive-zip-perl libbsd0
  libclone-perl libcroco3 libdebhelper-perl libelf1 libexpat1
  libfile-stripnondeterminism-perl libfile-which-perl libglib2.0-0 libicu63
  liblocal-lib-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libmodule-build-perl libmpdec2 libpipeline1 libpython3-stdlib
  libpython3.7-minimal libpython3.7-stdlib libsigsegv2 libssl1.1
  libsub-override-perl libtbb-dev libtbb2 libtest-deep-perl libtinfo5 libtool
  libuchardet0 libxml2 m4 man-db mime-support po-debconf python3
  python3-minimal python3.7 python3.7-minimal
  sbuild-build-depends-bowtie2-dummy sensible-utils zlib1g-dev
0 upgraded, 57 newly installed, 0 to remove and 29 not upgraded.
Need to get 25.6 MB of archives.
After this operation, 97.0 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-5Oaw9y/apt_archive ./ sbuild-build-depends-bowtie2-dummy 0.invalid.0 [924 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf liblocale-gettext-perl armhf 1.07-4 [18.1 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-3 [28.3 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.5-2 [584 kB]
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Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.5-2 [1527 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-1 [36.6 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.5-2 [1668 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.5-2 [347 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-1 [20.1 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-1 [61.5 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.2 [174 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.3-2 [1137 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.2 [1018 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.11 [180 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libclone-perl armhf 0.43-2 [14.4 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libmodule-build-perl all 0.422900-1 [258 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf liblocal-lib-perl all 2.000024-1 [53.7 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libtbb2 armhf 2019~U9-2 [115 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libtbb-dev armhf 2019~U9-2 [313 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libtest-deep-perl all 1.128-1 [48.8 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Processing triggers for libc-bin (2.29-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.15.0-58-generic armhf (armv8l)
Toolchain package versions: binutils_2.33.1-5+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-19+rpi1+b1 gcc-9_9.2.1-19+rpi1+b1 libc6-dev_2.29-3+rpi1 libstdc++-9-dev_9.2.1-19+rpi1+b1 libstdc++6_9.2.1-19+rpi1+b1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-5+rpi1 binutils-arm-linux-gnueabihf_2.33.1-5+rpi1 binutils-common_2.33.1-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-19+rpi1+b1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.2 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-19+rpi1+b1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-19+rpi1+b1 gcc-9-base_9.2.1-19+rpi1+b1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-4 gzip_1.9-3 help2man_1.47.11 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-19+rpi1+b1 libassuan0_2.5.3-7 libatomic1_9.2.1-19+rpi1+b1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-5+rpi1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-3+rpi1 libc-dev-bin_2.29-3+rpi1 libc6_2.29-3+rpi1 libc6-dev_2.29-3+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-19+rpi1+b1 libclone-perl_0.43-2 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.2 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libfile-which-perl_1.23-1 libgcc-9-dev_9.2.1-19+rpi1+b1 libgcc1_1:9.2.1-19+rpi1+b1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-5 libgomp1_9.2.1-19+rpi1+b1 libgpg-error0_1.36-7 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblocal-lib-perl_2.000024-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmodule-build-perl_0.422900-1 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-3 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.1-3 libpython3-stdlib_3.7.5-1 libpython3.7-minimal_3.7.5-2 libpython3.7-stdlib_3.7.5-2 libreadline7_7.0-5 libreadline8_8.0-3 librust-bitflags-dev_1.2.1-1 librust-cloudabi+default-dev_0.0.3-1 librust-cloudabi-dev_0.0.3-1 librust-fuchsia-zircon-dev_0.3.3-2 librust-fuchsia-zircon-sys-dev_0.3.3-2 librust-libc-dev_0.2.62-1 librust-phf-codegen-dev_0.7.23-1 librust-phf-generator-dev_0.7.23-1 librust-phf-shared-dev_0.7.23-2+b1 librust-rand-0.5+alloc-dev_0.5.5-2+rpi1 librust-rand-0.5+std-dev_0.5.5-2+rpi1 librust-rand-0.5-dev_0.5.5-2+rpi1 librust-rand-core-0.2+alloc-dev_0.2.2-1 librust-rand-core-0.2+std-dev_0.2.2-1 librust-rand-core-0.2-dev_0.2.2-1 librust-rand-core-dev_0.3.0-1 librust-siphasher-dev_0.2.3-1 librust-winapi-dev_0.3.6-1 librust-winapi-i686-pc-windows-gnu-dev_0.4.0-1 librust-winapi-x86-64-pc-windows-gnu-dev_0.4.0-1 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.2-2+rpi1 libselinux1_2.9-3 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-19+rpi1+b1 libstdc++6_9.2.1-19+rpi1+b1 libsub-override-perl_0.09-2 libsystemd0_243-8+rpi1 libtasn1-6_4.14-3 libtbb-dev_2019~U9-2 libtbb2_2019~U9-2 libtest-deep-perl_1.128-1 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-19+rpi1+b1 libuchardet0_0.0.6-3 libudev1_243-8+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_5.7 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python3_3.7.5-1 python3-minimal_3.7.5-1 python3.7_3.7.5-2 python3.7-minimal_3.7.5-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-bowtie2-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Dec 18 22:40:51 2019 UTC
gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bowtie2_2.3.5.1-6.dsc
dpkg-source: info: extracting bowtie2 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking bowtie2_2.3.5.1.orig.tar.xz
dpkg-source: info: unpacking bowtie2_2.3.5.1-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying drop-not-needed-js-from-manual.patch
dpkg-source: info: applying wrong-interpreter-path.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying reproducible.patch
dpkg-source: info: applying skip_test_requiring_non-free_libmath-random-perl.patch
dpkg-source: info: applying do-not-rebuild-during-test.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying silence_tbb_deprecation_warning.patch
dpkg-source: info: applying simde
dpkg-source: info: applying correct_64bit_test
dpkg-source: info: applying no_sanity

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-67f76782-ea37-429d-951b-2d50fc9b6622
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package bowtie2
dpkg-buildpackage: info: source version 2.3.5.1-6
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   dh_auto_clean
	make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-build-s-debug bowtie2-build-l-debug bowtie2-align-s-debug bowtie2-align-l-debug bowtie2-inspect-s-debug bowtie2-inspect-l-debug \
bowtie2-build-s.exe bowtie2-build-l.exe bowtie2-align-s.exe bowtie2-align-l.exe bowtie2-inspect-s.exe bowtie2-inspect-l.exe bowtie2-build-s-debug.exe bowtie2-build-l-debug.exe bowtie2-align-s-debug.exe bowtie2-align-l-debug.exe bowtie2-inspect-s-debug.exe bowtie2-inspect-l-debug.exe \
bowtie2-*.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
rm -rf .tmp
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- EXTRA_FLAGS="-std=c++98 -Wl,-z,relro -Wl,-z,now"  NO_TBB=1 POPCNT_CAPABILITY=
	make -j4 "INSTALL=install --strip-program=true" "EXTRA_FLAGS=-std=c++98 -Wl,-z,relro -Wl,-z,now" NO_TBB=1 POPCNT_CAPABILITY=
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -O3   -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DNDEBUG -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 \
	-o bowtie2-build-s bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
g++ -O3   -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 \
	-o bowtie2-build-l bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
g++ -O3   -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DNDEBUG -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 \
	-o bowtie2-align-s bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
g++ -O3   -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 \
	-o bowtie2-align-l bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
In file included from bt2_idx.h:42,
                 from bt2_build.cpp:28:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_search.cpp:40:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
diff_sample.h: In instantiation of ‘void DifferenceCoverSample<T>::build(int) [with TStr = SString<char>]’:
blockwise_sa.h:413:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
diff_sample.h:851:28: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  851 |      sanityCheckOrderedSufs(t, t.length(), sPrimeArr, sPrimeSz, v);
      |      ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff_sample.h:851:28: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
diff_sample.h: In instantiation of ‘void DifferenceCoverSample<T>::build(int) [with TStr = S2bDnaString]’:
blockwise_sa.h:413:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = S2bDnaString]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = S2bDnaString]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = S2bDnaString; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:647:74:   required from here
diff_sample.h:851:28: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList<unsigned int>*) [with T = SString<char>; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
diff_sample.h:800:18:   required from ‘void DifferenceCoverSample<T>::build(int) [with TStr = SString<char>]’
blockwise_sa.h:413:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
multikey_qsort.h:654:31: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  654 |         sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_build.cpp:28:
blockwise_sa.h: In instantiation of ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’:
blockwise_sa.h:661:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
blockwise_sa.h:498:15: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  498 |   mkeyQSortSuf(t, s, slen, 4,
      |   ~~~~~~~~~~~~^~~~~~~~~~~~~~~
  499 |                this->verbose(), this->sanityCheck());
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h:498:15: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList<unsigned int>*) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
diff_sample.h:800:18:   required from ‘void DifferenceCoverSample<T>::build(int) [with TStr = S2bDnaString]’
blockwise_sa.h:413:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = S2bDnaString]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = S2bDnaString]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = S2bDnaString; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:647:74:   required from here
multikey_qsort.h:654:31: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  654 |         sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:492:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:661:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = SString<char>; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:498:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:661:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:492:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:661:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:492:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:661:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:492:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:661:15:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from bt2_search.cpp:53:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from bt2_search.cpp:53:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_search.cpp:40:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_search.cpp:40:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_search.cpp:40:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
In file included from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_io.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_util.cpp:26:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
In file included from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
g++ -O3   -funroll-loops -g3 \
	-DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 -I . \
	-o bowtie2-inspect-s bt2_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
g++ -O3   -funroll-loops -g3 \
	-DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_INSPECT_MAIN  -DBOWTIE_64BIT_INDEX -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 -I . \
	-o bowtie2-inspect-l bt2_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
In file included from bt2_idx.h:42,
                 from bt2_inspect.cpp:29:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from bt2_idx.h:42,
                 from bt2_io.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_inspect.cpp:29:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_inspect.cpp:29:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_inspect.cpp:29:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_util.cpp:26:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
In file included from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_io.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_util.cpp:26:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from aligner_seed.cpp:23:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int, 128>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from aligner_cache.h:59,
                 from aligner_seed.cpp:20:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from aligner_seed.cpp:23:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from aligner_cache.h:59,
                 from aligner_seed.cpp:20:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from aligner_seed2.h:103,
                 from aligner_seed2.cpp:22:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from random_util.h:25,
                 from aligner_seed2.h:101,
                 from aligner_seed2.cpp:22:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from aligner_seed2.h:103,
                 from aligner_seed2.cpp:22:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from random_util.h:25,
                 from aligner_seed2.h:101,
                 from aligner_seed2.cpp:22:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_sw.cpp:25:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_sw.cpp:25:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_sw_driver.h:81,
                 from aligner_sw_driver.cpp:47:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_sw_driver.h:81,
                 from aligner_sw_driver.cpp:47:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from bt2_idx.h:42,
                 from group_walk.h:86,
                 from aligner_sw_driver.h:84,
                 from aligner_sw_driver.cpp:47:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int, 128>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from aligner_cache.h:59,
                 from aligner_sw_driver.cpp:46:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from group_walk.h:86,
                 from aligner_sw_driver.h:84,
                 from aligner_sw_driver.cpp:47:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from aligner_cache.h:59,
                 from aligner_sw_driver.cpp:46:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from aligner_bt.h:31,
                 from aligner_bt.cpp:20:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_bt.h:31,
                 from aligner_bt.cpp:20:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from sse_util.cpp:20:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_swsse.cpp:22:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from sse_util.cpp:20:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_swsse.cpp:22:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_loc_i16.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_loc_i16.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_ee_i16.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_ee_i16.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_loc_u8.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_loc_u8.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_ee_u8.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_ee_u8.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from bt2_idx.h:42,
                 from aligner_seed2.h:103,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from random_util.h:25,
                 from aligner_seed2.h:101,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from aligner_seed2.h:103,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from random_util.h:25,
                 from aligner_seed2.h:101,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make EXTRA_FLAGS="-std=c++98 -Wl,-z,relro -Wl,-z,now"  NO_TBB=1 POPCNT_CAPABILITY= \
  bowtie2-build-s-debug \
  bowtie2-build-l-debug \
  bowtie2-align-s-debug \
  bowtie2-align-l-debug \
  bowtie2-inspect-s-debug \
  bowtie2-inspect-l-debug
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -O0 -g3   -DCOMPILER_OPTIONS="\"-O0 -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 \
	-o bowtie2-build-s-debug bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
g++ -O0 -g3   -DCOMPILER_OPTIONS="\"-O0 -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 \
	-o bowtie2-build-l-debug bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
In file included from bt2_idx.h:42,
                 from bt2_build.cpp:28:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
diff_sample.h: In instantiation of ‘void DifferenceCoverSample<T>::build(int) [with TStr = SString<char>]’:
blockwise_sa.h:413:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
diff_sample.h:851:28: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  851 |      sanityCheckOrderedSufs(t, t.length(), sPrimeArr, sPrimeSz, v);
      |      ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff_sample.h:851:28: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from bt2_build.cpp:26:
blockwise_sa.h: In instantiation of ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’:
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
assert_helpers.h:72:12: warning: comparison of integer expressions of different signedness: ‘TIndexOffU’ {aka ‘long long unsigned int’} and ‘TIndexOff’ {aka ‘long long int’} [-Wsign-compare]
   72 |  if(!((ex) == (ac))) { \
      |      ~~~~~~^~~~~~~~
blockwise_sa.h:757:21: note: in expansion of macro ‘assert_eq’
  757 |                     assert_eq(numBuckets, _sampleSuffs.size()+1-added);
      |                     ^~~~~~~~~
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
diff_sample.h: In instantiation of ‘void DifferenceCoverSample<T>::build(int) [with TStr = S2bDnaString]’:
blockwise_sa.h:413:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = S2bDnaString]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = S2bDnaString]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = S2bDnaString; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:647:74:   required from here
diff_sample.h:851:28: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  851 |      sanityCheckOrderedSufs(t, t.length(), sPrimeArr, sPrimeSz, v);
      |      ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bt2_build.cpp:26:
blockwise_sa.h: In instantiation of ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = S2bDnaString]’:
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = S2bDnaString]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = S2bDnaString]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = S2bDnaString; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:647:74:   required from here
assert_helpers.h:72:12: warning: comparison of integer expressions of different signedness: ‘TIndexOffU’ {aka ‘long long unsigned int’} and ‘TIndexOff’ {aka ‘long long int’} [-Wsign-compare]
   72 |  if(!((ex) == (ac))) { \
      |      ~~~~~~^~~~~~~~
blockwise_sa.h:757:21: note: in expansion of macro ‘assert_eq’
  757 |                     assert_eq(numBuckets, _sampleSuffs.size()+1-added);
      |                     ^~~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList<unsigned int>*) [with T = SString<char>; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
diff_sample.h:800:18:   required from ‘void DifferenceCoverSample<T>::build(int) [with TStr = SString<char>]’
blockwise_sa.h:413:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
multikey_qsort.h:654:31: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  654 |         sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_build.cpp:28:
blockwise_sa.h: In instantiation of ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’:
blockwise_sa.h:661:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
blockwise_sa.h:498:15: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  498 |   mkeyQSortSuf(t, s, slen, 4,
      |   ~~~~~~~~~~~~^~~~~~~~~~~~~~~
  499 |                this->verbose(), this->sanityCheck());
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h:498:15: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList<unsigned int>*) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
diff_sample.h:800:18:   required from ‘void DifferenceCoverSample<T>::build(int) [with TStr = S2bDnaString]’
blockwise_sa.h:413:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = S2bDnaString]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = S2bDnaString]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = S2bDnaString; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:647:74:   required from here
multikey_qsort.h:654:31: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  654 |         sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:492:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:661:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = SString<char>; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:498:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:661:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:492:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:661:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:492:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:661:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:418:13:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:492:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:661:15:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
blockwise_sa.h:392:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:216:32:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1079:33:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:3:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:454:7:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:636:78:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
In file included from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_io.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_util.cpp:26:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
g++ -O0 -g3   \
	-DCOMPILER_OPTIONS="\"-O0 -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 \
	-o bowtie2-align-s-debug bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from bt2_search.cpp:53:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_sw.cpp:25:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_sw_driver.h:81,
                 from aligner_sw_driver.cpp:47:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_bt.h:31,
                 from aligner_bt.cpp:20:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from sse_util.cpp:20:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_swsse.cpp:22:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_loc_i16.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_ee_i16.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_loc_u8.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_ee_u8.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
g++ -O0 -g3   \
	-DCOMPILER_OPTIONS="\"-O0 -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 \
	-o bowtie2-align-l-debug bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
In file included from bt2_idx.h:42,
                 from bt2_search.cpp:40:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from bt2_search.cpp:53:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_search.cpp:40:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_search.cpp:40:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_search.cpp:40:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
In file included from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_io.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_util.cpp:26:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from aligner_seed.cpp:23:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int, 128>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from aligner_cache.h:59,
                 from aligner_seed.cpp:20:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from aligner_seed.cpp:23:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from aligner_cache.h:59,
                 from aligner_seed.cpp:20:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from aligner_seed2.h:103,
                 from aligner_seed2.cpp:22:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from random_util.h:25,
                 from aligner_seed2.h:101,
                 from aligner_seed2.cpp:22:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from aligner_seed2.h:103,
                 from aligner_seed2.cpp:22:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from random_util.h:25,
                 from aligner_seed2.h:101,
                 from aligner_seed2.cpp:22:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_sw.cpp:25:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_sw_driver.h:81,
                 from aligner_sw_driver.cpp:47:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from bt2_idx.h:42,
                 from group_walk.h:86,
                 from aligner_sw_driver.h:84,
                 from aligner_sw_driver.cpp:47:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int, 128>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from aligner_cache.h:59,
                 from aligner_sw_driver.cpp:46:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from group_walk.h:86,
                 from aligner_sw_driver.h:84,
                 from aligner_sw_driver.cpp:47:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from aligner_cache.h:59,
                 from aligner_sw_driver.cpp:46:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from aligner_bt.h:31,
                 from aligner_bt.cpp:20:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from sse_util.cpp:20:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_swsse.cpp:22:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_loc_i16.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_ee_i16.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_loc_u8.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from aligner_swsse.h:28,
                 from aligner_sw.h:84,
                 from aligner_swsse_ee_u8.cpp:56:
sse_util.h: In member function ‘__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:36: warning: ‘new’ of type ‘__m128i’ {aka ‘simde__m128i’} with extended alignment 16 [-Waligned-new=]
  220 |    last_alloc_ = new __m128i[sz + 2];
      |                                    ^
sse_util.h:220:36: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:36: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from bt2_idx.h:42,
                 from aligner_seed2.h:103,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from random_util.h:25,
                 from aligner_seed2.h:101,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from aligner_seed2.h:103,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from random_util.h:25,
                 from aligner_seed2.h:101,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
g++ -O0 -g3   \
	-DCOMPILER_OPTIONS="\"-O0 -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 -I . \
	-o bowtie2-inspect-s-debug bt2_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
g++ -O0 -g3   \
	-DCOMPILER_OPTIONS="\"-O0 -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98\"" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++98 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u -r NEWS`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DBOWTIE_INSPECT_MAIN -Wall \
	-Wdate-time -D_FORTIFY_SOURCE=2 -I . \
	-o bowtie2-inspect-l-debug bt2_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
	-Wl,-z,relro -Wl,-z,now -lz -lpthread
In file included from bt2_idx.h:42,
                 from bt2_inspect.cpp:29:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_inspect.cpp:29:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_inspect.cpp:29:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_inspect.cpp:29:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
alphabet.cpp:224:1: warning: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ is ill-formed in C++11 [-Wnarrowing]
  224 | };
      | ^
In file included from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_io.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
In file included from bt2_idx.h:42,
                 from bt2_util.cpp:26:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  529 |                this->verbose(), this->sanityCheck());
      |                                                    ^
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:529:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:63: note: in expansion of macro ‘OFF_MASK’
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                               ^~~~~~~~
In file included from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  757 |  if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:757:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:529:52:   required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |  if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                  ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:30,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1156:49: note: in expansion of macro ‘OFF_MASK’
 1156 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1165:49: note: in expansion of macro ‘OFF_MASK’
 1165 |    sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                 ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1067:40: note: in expansion of macro ‘OFF_MASK’
 1067 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1063:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1162:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:756:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:523:56:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:910:10: note: in expansion of macro ‘OFF_MASK’
  910 |    off = OFF_MASK;
      |          ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:919:29: note: in expansion of macro ‘OFF_MASK’
  919 |                             OFF_MASK, begin, end);
      |                             ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1003:48: note: in expansion of macro ‘OFF_MASK’
 1003 |   sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                ^~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make -j1 test
make[2]: Entering directory '/<<PKGBUILDDIR>>'
eval `perl -I /<<PKGBUILDDIR>>/.tmp/lib/perl5 -Mlocal::lib=/<<PKGBUILDDIR>>/.tmp` ; \
sh ./scripts/test/simple_tests.sh
Attempting to create directory /<<PKGBUILDDIR>>/.tmp
\1 better written as $1 at scripts/test/simple_tests.pl line 4671.
\1 better written as $1 at scripts/test/simple_tests.pl line 4672.
FASTA-continuous 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -F 10,9 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -F 10,9 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq2_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -F 10,9 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -F 10,9 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp .simple_tests.gz"
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz"
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -F 10,1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:12
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_1	0	0	2	255	10M	*	0	0	GCATCGATCA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_2	0	0	3	255	10M	*	0	0	CATCGATCAG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
Align should not fail when first seq in ref is all Ns (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNN
>1
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
./bowtie2     --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.0	SO:unsorted
@SQ	SN:1	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	1	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Align should not fail when multiple seqs are all Ns (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNN
>1
NNNNNNNNNNNNNNN
>2
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
./bowtie2     --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.0	SO:unsorted
@SQ	SN:2	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	2	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Should account for stretch of Ns at beginning (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:34
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	0	18	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	ABCDEDGHIJKLMNOP	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO
Error: Read 0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Cline 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ
Error: Read 0 has more quality values than read characters.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
trim-to: trim from 5'-end (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim-to 5:12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	7	255	12M	*	0	0	GATCAGTATCTG	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: trim from 3'-end (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim-to 3:12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: trim from 3'-end (default) (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim-to 12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: invalid position (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim-to 4:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

--trim-to: trim position must be either 3 or 5
Bowtie 2 version 2.3.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: 
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <i>        Files with interleaved paired-end FASTQ/FASTA reads
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <bam>      Files are unaligned BAM sorted by read name.
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  --tab5             query input files are TAB5 .tab5
  --tab6             query input files are TAB6 .tab6
  --qseq             query input files are in Illumina's qseq format
  -f                 query input files are (multi-)FASTA .fa/.mfa
  -r                 query input files are raw one-sequence-per-line
  -F k:<int>,i:<int> query input files are continuous FASTA where reads
                     are substrings (k-mers) extracted from a FASTA file <s>
                     and aligned at offsets 1, 1+i, 1+2i ... end of reference
  -c                 <m1>, <m2>, <r> are sequences themselves, not files
  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)
  -u/--upto <int>    stop after first <int> reads/pairs (no limit)
  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)
  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)
  --trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
                     If the read end is not specified then it defaults to 3 (0)
  --phred33          qualities are Phred+33 (default)
  --phred64          qualities are Phred+64
  --int-quals        qualities encoded as space-delimited integers

 Presets:                 Same as:
  For --end-to-end:
   --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
   --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
   --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
   --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

  For --local:
   --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
   --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
   --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
   --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

 Alignment:
  -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)
  -L <int>           length of seed substrings; must be >3, <32 (22)
  -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)
  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  --dpad <int>       include <int> extra ref chars on sides of DP table (15)
  --gbar <int>       disallow gaps within <int> nucs of read extremes (4)
  --ignore-quals     treat all quality values as 30 on Phred scale (off)
  --nofw             do not align forward (original) version of read (off)
  --norc             do not align reverse-complement version of read (off)
  --no-1mm-upfront   do not allow 1 mismatch alignments before attempting to
                     scan for the optimal seeded alignments
  --end-to-end       entire read must align; no clipping (on)
   OR
  --local            local alignment; ends might be soft clipped (off)

 Scoring:
  --ma <int>         match bonus (0 for --end-to-end, 2 for --local) 
  --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)
  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
  --rdg <int>,<int>  read gap open, extend penalties (5,3)
  --rfg <int>,<int>  reference gap open, extend penalties (5,3)
  --score-min <func> min acceptable alignment score w/r/t read length
                     (G,20,8 for local, L,-0.6,-0.6 for end-to-end)

 Reporting:
  (default)          look for multiple alignments, report best, with MAPQ
   OR
  -k <int>           report up to <int> alns per read; MAPQ not meaningful
   OR
  -a/--all           report all alignments; very slow, MAPQ not meaningful

 Effort:
  -D <int>           give up extending after <int> failed extends in a row (15)
  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)

 Paired-end:
  -I/--minins <int>  minimum fragment length (0)
  -X/--maxins <int>  maximum fragment length (500)
  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
  --no-mixed         suppress unpaired alignments for paired reads
  --no-discordant    suppress discordant alignments for paired reads
  --dovetail         concordant when mates extend past each other
  --no-contain       not concordant when one mate alignment contains other
  --no-overlap       not concordant when mates overlap at all

 BAM:
  --align-paired-reads Bowtie2 will, by default, attempt to align unpaired BAM reads.
                     Use this option to align paired-end reads instead.
  --preserve-tags    Preserve tags from the original BAM record by
                     appending them to the end of the corresponding SAM output.

 Output:
  -t/--time          print wall-clock time taken by search phases
  --un <path>        write unpaired reads that didn't align to <path>
  --al <path>        write unpaired reads that aligned at least once to <path>
  --un-conc <path>   write pairs that didn't align concordantly to <path>
  --al-conc <path>   write pairs that aligned concordantly at least once to <path>
    (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
    --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
  --quiet            print nothing to stderr except serious errors
  --met-file <path>  send metrics to file at <path> (off)
  --met-stderr       send metrics to stderr (off)
  --met <int>        report internal counters & metrics every <int> secs (1)
  --no-unal          suppress SAM records for unaligned reads
  --no-head          suppress header lines, i.e. lines starting with @
  --no-sq            suppress @SQ header lines
  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field
  --rg <text>        add <text> ("lab:value") to @RG line of SAM header.
                     Note: @RG line only printed when --rg-id is set.
  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.
  --sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace 
                      at the expense of generating non-standard SAM.
  --xeq              Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
  --soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN

 Performance:
  -p/--threads <int> number of alignment threads to launch (1)
  --reorder          force SAM output order to match order of input reads
  --mm               use memory-mapped I/O for index; many 'bowtie's can share

 Other:
  --qc-filter        filter out reads that are bad according to QSEQ filter
  --seed <int>       seed for random number generator (0)
  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes
  --version          print version information and quit
  -h/--help          print this usage message
Error: Encountered internal Bowtie 2 exception (#1)
Command: /<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 
(ERR): bowtie2-align exited with value 1
trim-to: invalid count (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim-to 5:-12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

--trim-to: the number bases to trim must be at least 0
Bowtie 2 version 2.3.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: 
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <i>        Files with interleaved paired-end FASTQ/FASTA reads
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <bam>      Files are unaligned BAM sorted by read name.
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  --tab5             query input files are TAB5 .tab5
  --tab6             query input files are TAB6 .tab6
  --qseq             query input files are in Illumina's qseq format
  -f                 query input files are (multi-)FASTA .fa/.mfa
  -r                 query input files are raw one-sequence-per-line
  -F k:<int>,i:<int> query input files are continuous FASTA where reads
                     are substrings (k-mers) extracted from a FASTA file <s>
                     and aligned at offsets 1, 1+i, 1+2i ... end of reference
  -c                 <m1>, <m2>, <r> are sequences themselves, not files
  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)
  -u/--upto <int>    stop after first <int> reads/pairs (no limit)
  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)
  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)
  --trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
                     If the read end is not specified then it defaults to 3 (0)
  --phred33          qualities are Phred+33 (default)
  --phred64          qualities are Phred+64
  --int-quals        qualities encoded as space-delimited integers

 Presets:                 Same as:
  For --end-to-end:
   --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
   --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
   --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
   --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

  For --local:
   --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
   --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
   --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
   --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

 Alignment:
  -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)
  -L <int>           length of seed substrings; must be >3, <32 (22)
  -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)
  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  --dpad <int>       include <int> extra ref chars on sides of DP table (15)
  --gbar <int>       disallow gaps within <int> nucs of read extremes (4)
  --ignore-quals     treat all quality values as 30 on Phred scale (off)
  --nofw             do not align forward (original) version of read (off)
  --norc             do not align reverse-complement version of read (off)
  --no-1mm-upfront   do not allow 1 mismatch alignments before attempting to
                     scan for the optimal seeded alignments
  --end-to-end       entire read must align; no clipping (on)
   OR
  --local            local alignment; ends might be soft clipped (off)

 Scoring:
  --ma <int>         match bonus (0 for --end-to-end, 2 for --local) 
  --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)
  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
  --rdg <int>,<int>  read gap open, extend penalties (5,3)
  --rfg <int>,<int>  reference gap open, extend penalties (5,3)
  --score-min <func> min acceptable alignment score w/r/t read length
                     (G,20,8 for local, L,-0.6,-0.6 for end-to-end)

 Reporting:
  (default)          look for multiple alignments, report best, with MAPQ
   OR
  -k <int>           report up to <int> alns per read; MAPQ not meaningful
   OR
  -a/--all           report all alignments; very slow, MAPQ not meaningful

 Effort:
  -D <int>           give up extending after <int> failed extends in a row (15)
  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)

 Paired-end:
  -I/--minins <int>  minimum fragment length (0)
  -X/--maxins <int>  maximum fragment length (500)
  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
  --no-mixed         suppress unpaired alignments for paired reads
  --no-discordant    suppress discordant alignments for paired reads
  --dovetail         concordant when mates extend past each other
  --no-contain       not concordant when one mate alignment contains other
  --no-overlap       not concordant when mates overlap at all

 BAM:
  --align-paired-reads Bowtie2 will, by default, attempt to align unpaired BAM reads.
                     Use this option to align paired-end reads instead.
  --preserve-tags    Preserve tags from the original BAM record by
                     appending them to the end of the corresponding SAM output.

 Output:
  -t/--time          print wall-clock time taken by search phases
  --un <path>        write unpaired reads that didn't align to <path>
  --al <path>        write unpaired reads that aligned at least once to <path>
  --un-conc <path>   write pairs that didn't align concordantly to <path>
  --al-conc <path>   write pairs that aligned concordantly at least once to <path>
    (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
    --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
  --quiet            print nothing to stderr except serious errors
  --met-file <path>  send metrics to file at <path> (off)
  --met-stderr       send metrics to stderr (off)
  --met <int>        report internal counters & metrics every <int> secs (1)
  --no-unal          suppress SAM records for unaligned reads
  --no-head          suppress header lines, i.e. lines starting with @
  --no-sq            suppress @SQ header lines
  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field
  --rg <text>        add <text> ("lab:value") to @RG line of SAM header.
                     Note: @RG line only printed when --rg-id is set.
  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.
  --sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace 
                      at the expense of generating non-standard SAM.
  --xeq              Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
  --soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN

 Performance:
  -p/--threads <int> number of alignment threads to launch (1)
  --reorder          force SAM output order to match order of input reads
  --mm               use memory-mapped I/O for index; many 'bowtie's can share

 Other:
  --qc-filter        filter out reads that are bad according to QSEQ filter
  --seed <int>       seed for random number generator (0)
  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes
  --version          print version information and quit
  -h/--help          print this usage message
Error: Encountered internal Bowtie 2 exception (#1)
Command: /<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 
(ERR): bowtie2-align exited with value 1
Cline 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Cline 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim5 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Cline 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
Cline multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII


@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Cline multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII


@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG


@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Cline paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Cline paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII"
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Cline paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Cline paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Fastq 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Fastq 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Fastq 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: reads file does not look like a FASTQ file
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Fastq 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Fastq 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Fastq 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz"
Fastq multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fastq multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fastq paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Fastq paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Fastq paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Fastq paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -3 7 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
r0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Fasta 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	15M	*	0	0	CATCGATCAGTATCT	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz
Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Fasta 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz
Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Fasta 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Fasta 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Fasta 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz"
Fasta multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	9M	=	9	19	AGCATCGAT	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YS:i:0	YT:Z:CP
Fasta paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	9M	=	9	19	AGCATCGAT	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YS:i:0	YT:Z:CP
Fasta paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Fasta paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Raw 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Raw 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Raw 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz"
Raw multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Raw multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Raw paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Raw paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Raw paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Raw paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Tabbed 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Tabbed 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
Error: Read r0 has more quality values than read characters.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Tabbed 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Tabbed 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim5 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Tabbed 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
Tabbed multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Tabbed multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Tabbed paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Tabbed paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Tabbed paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Tabbed paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
r0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Qseq 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Qseq 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
Qseq multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
MachName_RunNum_Lane_Tile_12_15_Index/0	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Qseq multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Qseq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
MachName_RunNum_Lane_Tile_12_15_Index/0	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Qseq paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index	99	0	1	255	10M	=	9	19	AGCATCGATC	ABCBGACBCB	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_10_10_Index	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	ABCBCAGBCBA	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	57865494859	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	163	0	1	255	10M	=	9	19	AGCATCGATC	AGGCBBGCBG	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Qseq paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz"
MachName_RunNum_Lane_Tile_12_15_Index	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	57865494859	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	163	0	1	255	10M	=	9	19	AGCATCGATC	AGGCBBGCBG	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Left-align insertion (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet  --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	23	24	2M1I40M	*	0	0	ACAAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-8	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:42	YT:Z:UU
Left-align deletion (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2     --quiet  --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	19	40	6M1D39M	*	0	0	ACGTACAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-8	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^A39	YT:Z:UU
Left-align insertion with mismatch at LHS (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet  --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	5	24	20M1D45M	*	0	0	TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:20^A0A44	YT:Z:UU
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet  --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1192
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	3	42	38M	=	1148	0	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UP
r0	129	0	1148	1	42M	=	3	0	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YT:Z:UP
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet  --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1028
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	3	42	38M	=	982	1021	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YS:i:0	YT:Z:DP
r0	129	0	982	42	42M	=	3	-1021	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YS:i:0	YT:Z:DP
MREVERSE flag is set if mate does not align (fw:1, sam:1)
References:
>0
TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet  --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:250
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	89	0	51	42	100M	=	51	0	TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:100	YT:Z:UP
r0	165	0	51	0	*	=	51	0	CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet  --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:290
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	3	1	38M	=	163	202	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YS:i:0	YT:Z:CP
r0	147	0	163	1	42M	=	3	-202	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YS:i:0	YT:Z:CP
MD:Z 1 (fw:1, sam:1)
References:
>0
CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0C39	YT:Z:UU
MD:Z 1 (fw:0, sam:1)
References:
>0
CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2     --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0C39	YT:Z:UU
MD:Z 2 (fw:1, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0A39	YT:Z:UU
MD:Z 2 (fw:0, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2     --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0A39	YT:Z:UU
MD:Z 3 (fw:1, sam:1)
References:
>0
CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:0	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^TA0A39	YT:Z:UU
MD:Z 3 (fw:0, sam:1)
References:
>0
CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2     --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:0	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^TA0A39	YT:Z:UU
MD:Z 4 (fw:1, sam:1)
References:
>0
CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-12	XN:i:3	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^NN0N39	YT:Z:UU
MD:Z 4 (fw:0, sam:1)
References:
>0
CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2     --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-12	XN:i:3	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^NN0N39	YT:Z:UU
Local alignment 1 (fw:1, sam:1)
References:
>0
TTGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	4M	*	0	0	TTGT	IIII	AS:i:8	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:4	YT:Z:UU
Local alignment 1 (fw:0, sam:1)
References:
>0
TTGT
./bowtie2    --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	4M	*	0	0	TTGT	IIII	AS:i:8	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:4	YT:Z:UU
Local alignment 2 (fw:1, sam:1)
References:
>0
TTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	3M1S	*	0	0	TTGT	IIII	AS:i:6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
Local alignment 2 (fw:0, sam:1)
References:
>0
TTGA
./bowtie2    --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	3M1S	*	0	0	TTGT	IIII	AS:i:6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
Local alignment 3 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	38	13M	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:26	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
r0	256	0	9	38	8M5S	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 3 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	38	13M	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:26	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
r0	272	0	9	38	8M5S	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 4 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	37	12M	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:24	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
r0	256	0	9	37	8M4S	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 4 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	37	12M	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:24	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
r0	272	0	9	37	8M4S	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Alignment order -k (fw:1, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	256	0	22	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	256	0	46	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	256	0	71	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -k (fw:0, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2    --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	272	0	22	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	272	0	46	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	272	0	71	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -a (fw:1, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2    --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	256	0	22	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	256	0	46	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	256	0	71	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -a (fw:0, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2    --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	272	0	22	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	272	0	46	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	272	0	71	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Mate reporting order, -a (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	99	0	205	1	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	147	0	270	1	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	1	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	270	1	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	1	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	68	1	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	83	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	163	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	1	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	3	1	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	1	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	205	1	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	68	1	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	3	1	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	99	0	307	255	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
r2	147	0	379	255	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
Mate reporting order, -a (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2     --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	83	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	163	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	1	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	3	1	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	1	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	205	1	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	68	1	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	3	1	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	99	0	205	1	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	147	0	270	1	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	1	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	270	1	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	1	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	68	1	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	83	0	379	255	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
r2	163	0	307	255	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
Mate reporting order, -M 1 (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2     --fr --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	99	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	147	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	83	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	163	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	99	0	307	42	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
r2	147	0	379	42	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
Mate reporting order, -M 1 (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2     --fr --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	83	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	163	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	99	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	147	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	83	0	379	42	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
r2	163	0	307	42	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
Non-overlapping; no args (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; no args (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-dovetail (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-dovetail (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-dovetail --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-overlap (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-overlap --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Overlapping; no args (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; no args (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-dovetail (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; --no-dovetail (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-dovetail --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-contain (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-contain --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; --no-contain (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-contain --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
r0	129	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:DP
Overlapping; --no-overlap (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-overlap --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:DP
r0	177	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
Scoring params 1 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:105
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	42	88M	*	0	0	GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:88	YT:Z:UU
Scoring params 1 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG
./bowtie2     --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:105
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	42	88M	*	0	0	GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:88	YT:Z:UU
Scoring params 2 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-38	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 2 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-38	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 3 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-31	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 3 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-31	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 4 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-30	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 4 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-30	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 5 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-40	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 5 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-40	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 6 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-41	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 6 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-41	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Q XS:i 1a (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-5	XS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-5	XS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,3 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,3 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,6 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,6 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,3 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,3 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,6 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,6 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-4	XS:i:-4	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-4	XS:i:-4	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
(fw:1, sam:1)
References:
>0
CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:68
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	73	0	2	255	27M	=	2	0	ATCGACTGAGACTCGTACGACAATTAC	IIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:27	YT:Z:UP
r0	133	0	2	0	*	=	2	0	TAGGTTTCGCGCGAAACGCTGGTGAT	IIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
(fw:0, sam:1)
References:
>0
CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT
./bowtie2     --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:68
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	137	0	2	255	27M	=	2	0	ATCGACTGAGACTCGTACGACAATTAC	IIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:27	YT:Z:UP
r0	69	0	2	0	*	=	2	0	TAGGTTTCGCGCGAAACGCTGGTGAT	IIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:528
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	217	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT
./bowtie2    --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:528
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	65	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2     --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2     --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2     --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 1 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
XS:i 1 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
XS:i 2 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-5 --quiet  --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGT	IIIIIIII	YT:Z:UU
XS:i 2 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-5 --quiet  --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACGAACAA	IIIIIIII	YT:Z:UU
XS:i 3a (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3a (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3b (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3b (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3c (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3c (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4a (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4b (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4b (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5a (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2    --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5b (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2    --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5b (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2    --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
BWA-SW-like 1 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --bwa-sw-like --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:56	YT:Z:UU
BWA-SW-like 1 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2    --bwa-sw-like --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:56	YT:Z:UU
BWA-SW-like 2 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2    --bwa-sw-like -L 18 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:48	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:26A0A28	YT:Z:UU
BWA-SW-like 2 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2    --bwa-sw-like -L 18 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:48	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:26A0A28	YT:Z:UU
BWA-SW-like 3 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2    --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	26M3D27M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:42	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:26^AAC27	YT:Z:UU
BWA-SW-like 3 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2    --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	26M3D27M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:42	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:26^AAC27	YT:Z:UU
SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	147	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	131	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --rf --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	163	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 1 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	147	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 2 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --rf --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	163	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 3 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	131	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	73	0	4	255	24M	=	4	0	CTATCTACGCTTCGGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:24	YT:Z:UP
r0	133	0	4	0	*	=	4	0	GATTGTCTTTTCCCGGAAAAATCGT	IIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
SAM paired-end where neither mate aligns (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CTATATACGAAAAAGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	GATTGTCTTTTCCCGGAAAAATCGT	IIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
SAM paired-end where both mates align, but discordantly (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:24	YS:i:0	YT:Z:DP
r0	129	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
matchesRef regression 4 (fw:1, sam:1)
References:
>0
CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC
>1
GCTCGGAATTCGTGCTCCGNCCCGTACGGTT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@SQ	SN:1	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UU
matchesRef regression 4 (fw:0, sam:1)
References:
>0
CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC
>1
GCTCGGAATTCGTGCTCCGNCCCGTACGGTT
./bowtie2    --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@SQ	SN:1	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UU
matchesRef regression 3 (fw:1, sam:1)
References:
>0
GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	10	255	38M	*	0	0	CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UU
matchesRef regression 3 (fw:0, sam:1)
References:
>0
GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC
./bowtie2    --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	10	255	38M	*	0	0	CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UU
matchesRef regression 2 (fw:1, sam:1)
References:
>0
GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG
>1
CCTTGTTNTTAATGCTGCCTGGTTTNG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@SQ	SN:1	LN:27
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
matchesRef regression 2 (fw:0, sam:1)
References:
>0
GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG
>1
CCTTGTTNTTAATGCTGCCTGGTTTNG
./bowtie2    --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@SQ	SN:1	LN:27
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	1	255	29S23M	=	1	-68	CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-78	XN:i:7	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:-128	YT:Z:CP
r0	163	0	1	255	45S15M	=	1	68	CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-128	XN:i:9	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:14T0	YS:i:-78	YT:Z:CP
matchesRef regression 1 (fw:1, sam:1)
References:
>0
AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:61
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	12	255	50M10S	*	0	0	AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:9	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU
matchesRef regression 1 (fw:0, sam:1)
References:
>0
AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC
./bowtie2    --overhang --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:61
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	12	255	50M10S	*	0	0	AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:9	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU
Discordant with different chromosomes (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCC
>1
CCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 35 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:23
@SQ	SN:1	LN:28
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	65	0	4	255	10M	1	8	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	1	8	255	10M	0	4	0	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	65	0	4	255	10M	1	7	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	129	1	7	255	10M	0	4	0	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Discordant with different chromosomes (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCC
>1
CCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2    -I 0 -X 35 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:23
@SQ	SN:1	LN:28
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	113	1	8	255	10M	0	4	0	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	1	8	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	113	1	7	255	10M	0	4	0	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	177	0	4	255	10M	1	7	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r1	99	0	1	255	10M	=	10	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	147	0	10	255	10M	=	1	-19	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r1	83	0	10	255	10M	=	1	-19	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	10	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 2 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r1	0	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r1	16	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --trim3 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	4	255	9M	*	0	0	ATCGATCAG	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --trim3 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	6	255	9M	*	0	0	CGATCAGTA	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --trim5 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	4	255	9M	*	0	0	ATCGATCAG	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --trim5 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	6	255	9M	*	0	0	CGATCAGTA	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:1, sam:1)
References:
>0
TGC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:3
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	1S3M	*	0	0	ATGC	IIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
(fw:0, sam:1)
References:
>0
TGC
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:3
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	1S3M	*	0	0	ATGC	IIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2     --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2     --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2     --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2     --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
r2	0	0	1	255	1S6M	*	0	0	ATTGTTC	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
r2	16	0	1	255	1S6M	*	0	0	ATTGTTC	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r2	4	*	0	0	*	*	0	0	GTTCGTA	IIIIIII	YT:Z:UU
r3	4	*	0	0	*	*	0	0	ATTGTTC	IIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r2	4	*	0	0	*	*	0	0	TACGAAC	IIIIIII	YT:Z:UU
r3	4	*	0	0	*	*	0	0	GAACAAT	IIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -X 1000 --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --local --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --local --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	1	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	487	1	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	1	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	724	1	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --fr --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	487	1	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	1	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	724	1	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	1	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --local --fr --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	1	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	487	1	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	1	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	724	1	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --local --fr --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	487	1	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	1	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	724	1	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	1	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -M 2 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --fr --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2     --fr --quiet -M 1 -X 150 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2     --fr --quiet -M 1 -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2     --fr --quiet -M 1 --local -X 150 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2     --fr --quiet -M 1 --local -X 150 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet -k 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2     --fr --quiet -k 1 -X 150 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --fr --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	42	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	42	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --fr --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	42	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	42	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --local --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	44	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	44	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --local --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	44	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	44	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:2607
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	961	1	33M	=	1027	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	1027	1	28M	=	961	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA
./bowtie2    -X 150 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:2607
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	2449	1	28M	=	2383	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	2383	1	33M	=	2449	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --local -X 150 --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1906
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	1672	1	33M	=	1738	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	1738	1	28M	=	1672	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC
./bowtie2    --local -X 150 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1906
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	1738	1	28M	=	1672	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	1672	1	33M	=	1738	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	42	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2     --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	42	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2    --local --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	44	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -M w/ 1 hit local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2    --local --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	44	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2     --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2     --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2    --local --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -m w/ 1 hit local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2    --local --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -M 2 --local --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -M 2 --local --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -k 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -X 150 --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    -X 150 --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -M 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	219	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	304	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	219	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	219	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	304	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	219	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
r0	256	0	1	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
r0	272	0	9	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCAT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATGAACAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2    --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
Gap penalties 1 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	6M1D6M	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	AS:i:-39	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^G6	YT:Z:UU
Gap penalties 1 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	6M1D6M	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	AS:i:-39	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^G6	YT:Z:UU
Gap penalties 2 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	YT:Z:UU
Gap penalties 2 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAAGAACAA	IIIIIIIIIIII	YT:Z:UU
Gap penalties 3 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
Gap penalties 3 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
Gap penalties 4 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 4 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAATCGAACAA	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 5 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 5 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAATCGAACAA	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 6 (fw:1, sam:1)
References:
>0
ATTGTTCGTTTGTTCGTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:18
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	6M1D5M1I6M	*	0	0	ATTGTTGTTTGATTCGTA	IIIIIIIIIIIIIIIIII	AS:i:-57	XN:i:0	XM:i:0	XO:i:2	XG:i:2	NM:i:2	MD:Z:6^C11	YT:Z:UU
Gap penalties 6 (fw:0, sam:1)
References:
>0
ATTGTTCGTTTGTTCGTA
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:18
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	6M1D5M1I6M	*	0	0	ATTGTTGTTTGATTCGTA	IIIIIIIIIIIIIIIIII	AS:i:-57	XN:i:0	XM:i:0	XO:i:2	XG:i:2	NM:i:2	MD:Z:6^C11	YT:Z:UU
Gap penalties 7 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTGTTTGATTCGT	IIIIIIIIIIIIIIII	YT:Z:UU
Gap penalties 7 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACGAATCAAACAACAA	IIIIIIIIIIIIIIII	YT:Z:UU
N filtering 1 (fw:1, sam:1)
References:
>0
GAGACTTTATACGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
N filtering 1 (fw:0, sam:1)
References:
>0
GAGACTTTATACGCATCGAACTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
N filtering 2 (fw:1, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 2 (fw:0, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 3 (fw:1, sam:1)
References:
>0
GAGACTTTATACGCATCGAANTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 3 (fw:0, sam:1)
References:
>0
GAGACTTTATACGCATCGAANTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 4 (fw:1, sam:1)
References:
>0
GAGACTTTNTACGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 4 (fw:0, sam:1)
References:
>0
GAGACTTTNTACGCATCGAACTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 5 (fw:1, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:2N10	YT:Z:UU
N filtering 5 (fw:0, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:2N10	YT:Z:UU
N filtering 6 (fw:1, sam:1)
References:
>0
GAGACTTTNTACGCATCGAANTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 6 (fw:0, sam:1)
References:
>0
GAGACTTTNTACGCATCGAANTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTTTGTTCGTTTG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	9M1I4M	*	0	0	TTTTGTTCGATTTG	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTTTGTTCGTTTG
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	9M1I4M	*	0	0	TTTTGTTCGATTTG	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	2M	*	0	0	CA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCA
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	2M	*	0	0	CA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (1) (fw:1, sam:1)
References:
>0
ACNCA
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	2M	*	0	0	AC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (1) (fw:0, sam:1)
References:
>0
ACNCA
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	2M	*	0	0	AC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (2) (fw:1, sam:1)
References:
>0
ACNCANNNNNNNNCGNNNNNNNNCG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:25
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (2) (fw:0, sam:1)
References:
>0
ACNCANNNNNNNNCGNNNNNNNNCG
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:25
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTYGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	1	255	8M	*	0	0	TTGTTGGT	IIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:5N2	YT:Z:UU
r1	0	0	1	255	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:5N2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATAACCTTCG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:10
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	4M2D4M	*	0	0	ATAATTCG	IIIIIIII	AS:i:-15	XN:i:0	XM:i:0	XO:i:1	XG:i:2	NM:i:2	MD:Z:4^CC4	YT:Z:UU
(fw:0, sam:1)
References:
>0
ATAACCTTCG
./bowtie2     --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:10
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	4M2D4M	*	0	0	ATAATTCG	IIIIIIII	AS:i:-15	XN:i:0	XM:i:0	XO:i:1	XG:i:2	NM:i:2	MD:Z:4^CC4	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATATGCCCCATGCCCCCCTCCG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:22
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	9M3D10M	*	0	0	ATATGCCCCCCCCCCTCCG	IIIIIIIIIIIIIIIIIII	AS:i:-20	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:9^ATG10	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATATGCCCCATGCCCCCCTCCG
./bowtie2     --quiet -a --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:22
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	9M3D10M	*	0	0	ATATGCCCCCCCCCCTCCG	IIIIIIIIIIIIIIIIIII	AS:i:-20	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:9^ATG10	YT:Z:UU
Simple paired-end 13 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	65	0	4	255	10M	=	30	36	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	129	0	30	255	10M	=	4	-36	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r2	67	0	4	255	10M	=	29	35	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r2	131	0	29	255	10M	=	4	-35	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	67	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	131	0	28	255	10M	=	4	-34	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r4	65	0	5	255	10M	=	31	36	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r4	129	0	31	255	10M	=	5	-36	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r5	67	0	5	255	10M	=	30	35	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r5	131	0	30	255	10M	=	5	-35	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	67	0	5	255	10M	=	29	34	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	131	0	29	255	10M	=	5	-34	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	67	0	5	255	10M	=	28	33	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	131	0	28	255	10M	=	5	-33	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 13 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2    -I 0 -X 35 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz"
r0	113	0	31	255	10M	=	4	-37	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	113	0	30	255	10M	=	4	-36	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	177	0	4	255	10M	=	30	36	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r2	115	0	29	255	10M	=	4	-35	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r2	179	0	4	255	10M	=	29	35	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	115	0	28	255	10M	=	4	-34	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	179	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r4	113	0	31	255	10M	=	5	-36	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r4	177	0	5	255	10M	=	31	36	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r5	115	0	30	255	10M	=	5	-35	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r5	179	0	5	255	10M	=	30	35	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	115	0	29	255	10M	=	5	-34	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	179	0	5	255	10M	=	29	34	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	115	0	28	255	10M	=	5	-33	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	179	0	5	255	10M	=	28	33	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 12 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	GGCCCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	67	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	131	0	28	255	10M	=	4	-34	CCGGGCCCGC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 12 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC
./bowtie2    -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	113	0	31	255	10M	=	4	-37	GGCCCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	115	0	28	255	10M	=	4	-34	CCGGGCCCGC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	179	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 11 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 11 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2    -I 0 -X 36 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	31	255	10M	=	4	-37	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 10 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 28 -X 80 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:41
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	10M	=	21	27	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	21	255	10M	=	4	-27	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 10 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2    -I 28 -X 80 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:41
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	21	255	10M	=	4	-27	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	21	27	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 9 (fw:1, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	38	1	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	60	1	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 9 (fw:0, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2    -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	60	1	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	163	0	38	1	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 8 (fw:1, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 80 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	1	10M	=	60	66	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	60	1	10M	=	4	-66	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	355	0	38	1	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	403	0	60	1	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	355	0	20	1	10M	=	60	50	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	403	0	60	1	10M	=	20	-50	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 8 (fw:0, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2    -I 0 -X 80 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	60	1	10M	=	4	-66	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	163	0	4	1	10M	=	60	66	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	339	0	60	1	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	419	0	38	1	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	339	0	60	1	10M	=	20	-50	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	419	0	20	1	10M	=	60	50	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 2; no --no-mixed (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	153	0	4	255	10M	=	4	0	ATATATATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UP
r0	101	0	4	0	*	=	4	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
Simple paired-end 2; --no-mixed (fw:1, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	ATATATATAT	IIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
Simple paired-end 2; --no-mixed (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC
./bowtie2    -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	ATATATATAT	IIIIIIIIII	YT:Z:UP
Simple paired-end 1 (fw:1, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 50 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	10M	=	36	42	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	131	0	36	255	10M	=	4	-42	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 1 (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC
./bowtie2    -I 0 -X 50 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	36	255	10M	=	4	-42	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	179	0	4	255	10M	=	36	42	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:1, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2     --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2     --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2     --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy SEED=0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy SEED=0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	256	0	9	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	256	0	5	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-3	XS:i:-2	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:1C0G2T2	YT:Z:UU
r0	256	0	8	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2T0G1T0C0G0	YT:Z:UU
r0	256	0	6	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:0C0G0T2G0T1	YT:Z:UU
r0	256	0	4	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2C0G1T0T0G0	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	272	0	1	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	272	0	5	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-3	XS:i:-2	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:1C0G2T2	YT:Z:UU
r0	272	0	8	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2T0G1T0C0G0	YT:Z:UU
r0	272	0	4	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2C0G1T0T0G0	YT:Z:UU
r0	272	0	6	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:0C0G0T2G0T1	YT:Z:UU
FASTA-continuous 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -F 10,9 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -F 10,9 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq2_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -F 10,9 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -F 10,9 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz"
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz"
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -F 10,1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:12
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_1	0	0	2	255	10M	*	0	0	GCATCGATCA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_2	0	0	3	255	10M	*	0	0	CATCGATCAG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
Align should not fail when first seq in ref is all Ns (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNN
>1
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
./bowtie2 --debug    --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.0	SO:unsorted
@SQ	SN:1	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	1	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Align should not fail when multiple seqs are all Ns (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNN
>1
NNNNNNNNNNNNNNN
>2
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
./bowtie2 --debug    --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.0	SO:unsorted
@SQ	SN:2	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	2	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Should account for stretch of Ns at beginning (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:34
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	0	18	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	ABCDEDGHIJKLMNOP	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO
Error: Read 0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Cline 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ
Error: Read 0 has more quality values than read characters.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
trim-to: trim from 5'-end (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim-to 5:12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	7	255	12M	*	0	0	GATCAGTATCTG	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: trim from 3'-end (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim-to 3:12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: trim from 3'-end (default) (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim-to 12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: invalid position (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim-to 4:12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

--trim-to: trim position must be either 3 or 5
Bowtie 2 version 2.3.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: 
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <i>        Files with interleaved paired-end FASTQ/FASTA reads
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <bam>      Files are unaligned BAM sorted by read name.
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  --tab5             query input files are TAB5 .tab5
  --tab6             query input files are TAB6 .tab6
  --qseq             query input files are in Illumina's qseq format
  -f                 query input files are (multi-)FASTA .fa/.mfa
  -r                 query input files are raw one-sequence-per-line
  -F k:<int>,i:<int> query input files are continuous FASTA where reads
                     are substrings (k-mers) extracted from a FASTA file <s>
                     and aligned at offsets 1, 1+i, 1+2i ... end of reference
  -c                 <m1>, <m2>, <r> are sequences themselves, not files
  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)
  -u/--upto <int>    stop after first <int> reads/pairs (no limit)
  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)
  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)
  --trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
                     If the read end is not specified then it defaults to 3 (0)
  --phred33          qualities are Phred+33 (default)
  --phred64          qualities are Phred+64
  --int-quals        qualities encoded as space-delimited integers

 Presets:                 Same as:
  For --end-to-end:
   --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
   --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
   --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
   --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

  For --local:
   --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
   --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
   --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
   --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

 Alignment:
  -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)
  -L <int>           length of seed substrings; must be >3, <32 (22)
  -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)
  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  --dpad <int>       include <int> extra ref chars on sides of DP table (15)
  --gbar <int>       disallow gaps within <int> nucs of read extremes (4)
  --ignore-quals     treat all quality values as 30 on Phred scale (off)
  --nofw             do not align forward (original) version of read (off)
  --norc             do not align reverse-complement version of read (off)
  --no-1mm-upfront   do not allow 1 mismatch alignments before attempting to
                     scan for the optimal seeded alignments
  --end-to-end       entire read must align; no clipping (on)
   OR
  --local            local alignment; ends might be soft clipped (off)

 Scoring:
  --ma <int>         match bonus (0 for --end-to-end, 2 for --local) 
  --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)
  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
  --rdg <int>,<int>  read gap open, extend penalties (5,3)
  --rfg <int>,<int>  reference gap open, extend penalties (5,3)
  --score-min <func> min acceptable alignment score w/r/t read length
                     (G,20,8 for local, L,-0.6,-0.6 for end-to-end)

 Reporting:
  (default)          look for multiple alignments, report best, with MAPQ
   OR
  -k <int>           report up to <int> alns per read; MAPQ not meaningful
   OR
  -a/--all           report all alignments; very slow, MAPQ not meaningful

 Effort:
  -D <int>           give up extending after <int> failed extends in a row (15)
  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)

 Paired-end:
  -I/--minins <int>  minimum fragment length (0)
  -X/--maxins <int>  maximum fragment length (500)
  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
  --no-mixed         suppress unpaired alignments for paired reads
  --no-discordant    suppress discordant alignments for paired reads
  --dovetail         concordant when mates extend past each other
  --no-contain       not concordant when one mate alignment contains other
  --no-overlap       not concordant when mates overlap at all

 BAM:
  --align-paired-reads Bowtie2 will, by default, attempt to align unpaired BAM reads.
                     Use this option to align paired-end reads instead.
  --preserve-tags    Preserve tags from the original BAM record by
                     appending them to the end of the corresponding SAM output.

 Output:
  -t/--time          print wall-clock time taken by search phases
  --un <path>        write unpaired reads that didn't align to <path>
  --al <path>        write unpaired reads that aligned at least once to <path>
  --un-conc <path>   write pairs that didn't align concordantly to <path>
  --al-conc <path>   write pairs that aligned concordantly at least once to <path>
    (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
    --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
  --quiet            print nothing to stderr except serious errors
  --met-file <path>  send metrics to file at <path> (off)
  --met-stderr       send metrics to stderr (off)
  --met <int>        report internal counters & metrics every <int> secs (1)
  --no-unal          suppress SAM records for unaligned reads
  --no-head          suppress header lines, i.e. lines starting with @
  --no-sq            suppress @SQ header lines
  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field
  --rg <text>        add <text> ("lab:value") to @RG line of SAM header.
                     Note: @RG line only printed when --rg-id is set.
  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.
  --sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace 
                      at the expense of generating non-standard SAM.
  --xeq              Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
  --soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN

 Performance:
  -p/--threads <int> number of alignment threads to launch (1)
  --reorder          force SAM output order to match order of input reads
  --mm               use memory-mapped I/O for index; many 'bowtie's can share

 Other:
  --qc-filter        filter out reads that are bad according to QSEQ filter
  --seed <int>       seed for random number generator (0)
  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes
  --version          print version information and quit
  -h/--help          print this usage message
Error: Encountered internal Bowtie 2 exception (#1)
Command: /<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 
(ERR): bowtie2-align exited with value 1
trim-to: invalid count (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim-to 5:-12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

--trim-to: the number bases to trim must be at least 0
Bowtie 2 version 2.3.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: 
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <i>        Files with interleaved paired-end FASTQ/FASTA reads
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <bam>      Files are unaligned BAM sorted by read name.
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  --tab5             query input files are TAB5 .tab5
  --tab6             query input files are TAB6 .tab6
  --qseq             query input files are in Illumina's qseq format
  -f                 query input files are (multi-)FASTA .fa/.mfa
  -r                 query input files are raw one-sequence-per-line
  -F k:<int>,i:<int> query input files are continuous FASTA where reads
                     are substrings (k-mers) extracted from a FASTA file <s>
                     and aligned at offsets 1, 1+i, 1+2i ... end of reference
  -c                 <m1>, <m2>, <r> are sequences themselves, not files
  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)
  -u/--upto <int>    stop after first <int> reads/pairs (no limit)
  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)
  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)
  --trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
                     If the read end is not specified then it defaults to 3 (0)
  --phred33          qualities are Phred+33 (default)
  --phred64          qualities are Phred+64
  --int-quals        qualities encoded as space-delimited integers

 Presets:                 Same as:
  For --end-to-end:
   --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
   --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
   --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
   --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

  For --local:
   --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
   --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
   --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
   --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

 Alignment:
  -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)
  -L <int>           length of seed substrings; must be >3, <32 (22)
  -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)
  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  --dpad <int>       include <int> extra ref chars on sides of DP table (15)
  --gbar <int>       disallow gaps within <int> nucs of read extremes (4)
  --ignore-quals     treat all quality values as 30 on Phred scale (off)
  --nofw             do not align forward (original) version of read (off)
  --norc             do not align reverse-complement version of read (off)
  --no-1mm-upfront   do not allow 1 mismatch alignments before attempting to
                     scan for the optimal seeded alignments
  --end-to-end       entire read must align; no clipping (on)
   OR
  --local            local alignment; ends might be soft clipped (off)

 Scoring:
  --ma <int>         match bonus (0 for --end-to-end, 2 for --local) 
  --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)
  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
  --rdg <int>,<int>  read gap open, extend penalties (5,3)
  --rfg <int>,<int>  reference gap open, extend penalties (5,3)
  --score-min <func> min acceptable alignment score w/r/t read length
                     (G,20,8 for local, L,-0.6,-0.6 for end-to-end)

 Reporting:
  (default)          look for multiple alignments, report best, with MAPQ
   OR
  -k <int>           report up to <int> alns per read; MAPQ not meaningful
   OR
  -a/--all           report all alignments; very slow, MAPQ not meaningful

 Effort:
  -D <int>           give up extending after <int> failed extends in a row (15)
  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)

 Paired-end:
  -I/--minins <int>  minimum fragment length (0)
  -X/--maxins <int>  maximum fragment length (500)
  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
  --no-mixed         suppress unpaired alignments for paired reads
  --no-discordant    suppress discordant alignments for paired reads
  --dovetail         concordant when mates extend past each other
  --no-contain       not concordant when one mate alignment contains other
  --no-overlap       not concordant when mates overlap at all

 BAM:
  --align-paired-reads Bowtie2 will, by default, attempt to align unpaired BAM reads.
                     Use this option to align paired-end reads instead.
  --preserve-tags    Preserve tags from the original BAM record by
                     appending them to the end of the corresponding SAM output.

 Output:
  -t/--time          print wall-clock time taken by search phases
  --un <path>        write unpaired reads that didn't align to <path>
  --al <path>        write unpaired reads that aligned at least once to <path>
  --un-conc <path>   write pairs that didn't align concordantly to <path>
  --al-conc <path>   write pairs that aligned concordantly at least once to <path>
    (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
    --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
  --quiet            print nothing to stderr except serious errors
  --met-file <path>  send metrics to file at <path> (off)
  --met-stderr       send metrics to stderr (off)
  --met <int>        report internal counters & metrics every <int> secs (1)
  --no-unal          suppress SAM records for unaligned reads
  --no-head          suppress header lines, i.e. lines starting with @
  --no-sq            suppress @SQ header lines
  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field
  --rg <text>        add <text> ("lab:value") to @RG line of SAM header.
                     Note: @RG line only printed when --rg-id is set.
  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.
  --sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace 
                      at the expense of generating non-standard SAM.
  --xeq              Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
  --soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN

 Performance:
  -p/--threads <int> number of alignment threads to launch (1)
  --reorder          force SAM output order to match order of input reads
  --mm               use memory-mapped I/O for index; many 'bowtie's can share

 Other:
  --qc-filter        filter out reads that are bad according to QSEQ filter
  --seed <int>       seed for random number generator (0)
  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes
  --version          print version information and quit
  -h/--help          print this usage message
Error: Encountered internal Bowtie 2 exception (#1)
Command: /<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 
(ERR): bowtie2-align exited with value 1
Cline 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Cline 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim5 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Cline 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
Cline multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII


@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Cline multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII


@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG


@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Cline paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Cline paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII"
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Cline paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Cline paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Fastq 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Fastq 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Fastq 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: reads file does not look like a FASTQ file
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Fastq 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Fastq 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Fastq 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz"
Fastq multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fastq multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fastq paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Fastq paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Fastq paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Fastq paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
r0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Fasta 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	15M	*	0	0	CATCGATCAGTATCT	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz
Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Fasta 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz
Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Fasta 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Fasta 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim3 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Fasta 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz"
Fasta multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	9M	=	9	19	AGCATCGAT	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YS:i:0	YT:Z:CP
Fasta paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	9M	=	9	19	AGCATCGAT	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YS:i:0	YT:Z:CP
Fasta paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Fasta paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -3 7 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Raw 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Raw 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim3 16 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Raw 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz"
Raw multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Raw multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Raw paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Raw paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Raw paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Raw paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -3 7 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Tabbed 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Tabbed 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
Error: Read r0 has more quality values than read characters.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Tabbed 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Tabbed 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim5 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Tabbed 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
Tabbed multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Tabbed multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Tabbed paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Tabbed paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Tabbed paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Tabbed paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -3 7 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
r0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Qseq 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
Qseq 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   --trim3 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
Qseq multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug    --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
MachName_RunNum_Lane_Tile_12_15_Index/0	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Qseq multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Qseq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
MachName_RunNum_Lane_Tile_12_15_Index/0	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Qseq paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index	99	0	1	255	10M	=	9	19	AGCATCGATC	ABCBGACBCB	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_10_10_Index	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	ABCBCAGBCBA	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	57865494859	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	163	0	1	255	10M	=	9	19	AGCATCGATC	AGGCBBGCBG	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Qseq paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz"
MachName_RunNum_Lane_Tile_12_15_Index	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	57865494859	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	163	0	1	255	10M	=	9	19	AGCATCGATC	AGGCBBGCBG	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Left-align insertion (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet  --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	23	24	2M1I40M	*	0	0	ACAAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-8	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:42	YT:Z:UU
Left-align deletion (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2 --debug    --quiet  --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	19	40	6M1D39M	*	0	0	ACGTACAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-8	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^A39	YT:Z:UU
Left-align insertion with mismatch at LHS (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet  --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	5	24	20M1D45M	*	0	0	TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:20^A0A44	YT:Z:UU
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --fr --quiet  --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1192
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	3	42	38M	=	1148	0	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UP
r0	129	0	1148	1	42M	=	3	0	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YT:Z:UP
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --fr --quiet  --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1028
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	3	42	38M	=	982	1021	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YS:i:0	YT:Z:DP
r0	129	0	982	42	42M	=	3	-1021	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YS:i:0	YT:Z:DP
MREVERSE flag is set if mate does not align (fw:1, sam:1)
References:
>0
TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --fr --quiet  --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:250
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	89	0	51	42	100M	=	51	0	TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:100	YT:Z:UP
r0	165	0	51	0	*	=	51	0	CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --fr --quiet  --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:290
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	3	1	38M	=	163	202	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YS:i:0	YT:Z:CP
r0	147	0	163	1	42M	=	3	-202	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YS:i:0	YT:Z:CP
MD:Z 1 (fw:1, sam:1)
References:
>0
CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0C39	YT:Z:UU
MD:Z 1 (fw:0, sam:1)
References:
>0
CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2 --debug    --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0C39	YT:Z:UU
MD:Z 2 (fw:1, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0A39	YT:Z:UU
MD:Z 2 (fw:0, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2 --debug    --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0A39	YT:Z:UU
MD:Z 3 (fw:1, sam:1)
References:
>0
CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:0	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^TA0A39	YT:Z:UU
MD:Z 3 (fw:0, sam:1)
References:
>0
CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2 --debug    --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:0	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^TA0A39	YT:Z:UU
MD:Z 4 (fw:1, sam:1)
References:
>0
CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-12	XN:i:3	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^NN0N39	YT:Z:UU
MD:Z 4 (fw:0, sam:1)
References:
>0
CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2 --debug    --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-12	XN:i:3	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^NN0N39	YT:Z:UU
Local alignment 1 (fw:1, sam:1)
References:
>0
TTGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	4M	*	0	0	TTGT	IIII	AS:i:8	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:4	YT:Z:UU
Local alignment 1 (fw:0, sam:1)
References:
>0
TTGT
./bowtie2 --debug   --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	4M	*	0	0	TTGT	IIII	AS:i:8	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:4	YT:Z:UU
Local alignment 2 (fw:1, sam:1)
References:
>0
TTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	3M1S	*	0	0	TTGT	IIII	AS:i:6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
Local alignment 2 (fw:0, sam:1)
References:
>0
TTGA
./bowtie2 --debug   --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	3M1S	*	0	0	TTGT	IIII	AS:i:6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
Local alignment 3 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	38	13M	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:26	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
r0	256	0	9	38	8M5S	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 3 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	38	13M	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:26	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
r0	272	0	9	38	8M5S	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 4 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	37	12M	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:24	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
r0	256	0	9	37	8M4S	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 4 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	37	12M	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:24	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
r0	272	0	9	37	8M4S	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Alignment order -k (fw:1, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	256	0	22	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	256	0	46	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	256	0	71	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -k (fw:0, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2 --debug   --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	272	0	22	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	272	0	46	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	272	0	71	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -a (fw:1, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2 --debug   --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	256	0	22	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	256	0	46	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	256	0	71	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -a (fw:0, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2 --debug   --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	272	0	22	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	272	0	46	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	272	0	71	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Mate reporting order, -a (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	99	0	205	1	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	147	0	270	1	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	1	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	270	1	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	1	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	68	1	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	83	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	163	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	1	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	3	1	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	1	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	205	1	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	68	1	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	3	1	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	99	0	307	255	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
r2	147	0	379	255	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
Mate reporting order, -a (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2 --debug    --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	83	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	163	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	1	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	3	1	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	1	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	205	1	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	68	1	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	3	1	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	99	0	205	1	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	147	0	270	1	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	1	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	270	1	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	1	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	68	1	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	83	0	379	255	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
r2	163	0	307	255	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
Mate reporting order, -M 1 (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2 --debug    --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	99	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	147	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	83	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	163	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	99	0	307	42	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
r2	147	0	379	42	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
Mate reporting order, -M 1 (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2 --debug    --fr --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	83	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	163	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	99	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	147	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	83	0	379	42	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
r2	163	0	307	42	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
Non-overlapping; no args (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; no args (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug    --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug    --ff --quiet -M 1 --no-discordant --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug    --ff --quiet -M 1 --no-discordant --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug    --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug    --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug    --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug    --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-dovetail (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-dovetail (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --no-overlap --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-overlap (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Overlapping; no args (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug    --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; no args (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug    --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-dovetail (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --no-dovetail --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; --no-dovetail (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-contain (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --no-contain --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; --no-contain (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --no-contain --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --no-overlap --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
r0	129	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:DP
Overlapping; --no-overlap (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug   --no-overlap --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:DP
r0	177	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
Scoring params 1 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:105
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	42	88M	*	0	0	GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:88	YT:Z:UU
Scoring params 1 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:105
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	42	88M	*	0	0	GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:88	YT:Z:UU
Scoring params 2 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-38	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 2 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --debug   --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-38	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 3 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --debug   --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-31	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 3 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --debug   --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-31	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 4 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --debug   --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-30	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 4 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --debug   --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-30	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 5 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --debug   --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-40	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 5 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --debug   --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-40	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 6 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --debug   --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-41	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 6 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --debug   --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-41	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Q XS:i 1a (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-5	XS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-5	XS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,3 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,3 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,6 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,6 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,3 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,3 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,6 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,6 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-4	XS:i:-4	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-4	XS:i:-4	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
(fw:1, sam:1)
References:
>0
CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:68
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	73	0	2	255	27M	=	2	0	ATCGACTGAGACTCGTACGACAATTAC	IIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:27	YT:Z:UP
r0	133	0	2	0	*	=	2	0	TAGGTTTCGCGCGAAACGCTGGTGAT	IIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
(fw:0, sam:1)
References:
>0
CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT
./bowtie2 --debug    --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:68
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	137	0	2	255	27M	=	2	0	ATCGACTGAGACTCGTACGACAATTAC	IIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:27	YT:Z:UP
r0	69	0	2	0	*	=	2	0	TAGGTTTCGCGCGAAACGCTGGTGAT	IIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:528
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	217	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT
./bowtie2 --debug   --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:528
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	65	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 1 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
XS:i 1 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
XS:i 2 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-5 --quiet  --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGT	IIIIIIII	YT:Z:UU
XS:i 2 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-5 --quiet  --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACGAACAA	IIIIIIII	YT:Z:UU
XS:i 3a (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3a (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3b (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3b (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3c (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3c (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2 --debug   --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4a (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2 --debug   --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4b (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2 --debug   --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4b (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2 --debug   --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5a (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2 --debug   --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5b (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2 --debug   --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5b (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2 --debug   --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
BWA-SW-like 1 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --bwa-sw-like --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:56	YT:Z:UU
BWA-SW-like 1 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --debug   --bwa-sw-like --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:56	YT:Z:UU
BWA-SW-like 2 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --debug   --bwa-sw-like -L 18 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:48	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:26A0A28	YT:Z:UU
BWA-SW-like 2 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --debug   --bwa-sw-like -L 18 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:48	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:26A0A28	YT:Z:UU
BWA-SW-like 3 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --debug   --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	26M3D27M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:42	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:26^AAC27	YT:Z:UU
BWA-SW-like 3 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --debug   --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	26M3D27M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:42	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:26^AAC27	YT:Z:UU
SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	147	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --debug    --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	131	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --debug    --rf --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --rf --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	163	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 1 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --debug    --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	147	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 2 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --debug    --rf --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --rf --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	163	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 3 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --debug    --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	131	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --debug    --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	73	0	4	255	24M	=	4	0	CTATCTACGCTTCGGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:24	YT:Z:UP
r0	133	0	4	0	*	=	4	0	GATTGTCTTTTCCCGGAAAAATCGT	IIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
SAM paired-end where neither mate aligns (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --debug    --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CTATATACGAAAAAGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	GATTGTCTTTTCCCGGAAAAATCGT	IIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
SAM paired-end where both mates align, but discordantly (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --debug    --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:24	YS:i:0	YT:Z:DP
r0	129	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
matchesRef regression 4 (fw:1, sam:1)
References:
>0
CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC
>1
GCTCGGAATTCGTGCTCCGNCCCGTACGGTT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@SQ	SN:1	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UU
matchesRef regression 4 (fw:0, sam:1)
References:
>0
CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC
>1
GCTCGGAATTCGTGCTCCGNCCCGTACGGTT
./bowtie2 --debug   --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:120
@SQ	SN:1	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UU
matchesRef regression 3 (fw:1, sam:1)
References:
>0
GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	10	255	38M	*	0	0	CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UU
matchesRef regression 3 (fw:0, sam:1)
References:
>0
GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC
./bowtie2 --debug   --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	10	255	38M	*	0	0	CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UU
matchesRef regression 2 (fw:1, sam:1)
References:
>0
GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG
>1
CCTTGTTNTTAATGCTGCCTGGTTTNG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@SQ	SN:1	LN:27
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
matchesRef regression 2 (fw:0, sam:1)
References:
>0
GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG
>1
CCTTGTTNTTAATGCTGCCTGGTTTNG
./bowtie2 --debug   --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:47
@SQ	SN:1	LN:27
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	1	255	29S23M	=	1	-68	CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-78	XN:i:7	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:-128	YT:Z:CP
r0	163	0	1	255	45S15M	=	1	68	CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-128	XN:i:9	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:14T0	YS:i:-78	YT:Z:CP
matchesRef regression 1 (fw:1, sam:1)
References:
>0
AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:61
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	12	255	50M10S	*	0	0	AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:9	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU
matchesRef regression 1 (fw:0, sam:1)
References:
>0
AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC
./bowtie2 --debug   --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:61
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	12	255	50M10S	*	0	0	AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:9	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU
Discordant with different chromosomes (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCC
>1
CCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:23
@SQ	SN:1	LN:28
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	65	0	4	255	10M	1	8	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	1	8	255	10M	0	4	0	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	65	0	4	255	10M	1	7	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	129	1	7	255	10M	0	4	0	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Discordant with different chromosomes (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCC
>1
CCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2 --debug   -I 0 -X 35 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:23
@SQ	SN:1	LN:28
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	113	1	8	255	10M	0	4	0	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	1	8	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	113	1	7	255	10M	0	4	0	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	177	0	4	255	10M	1	7	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r1	99	0	1	255	10M	=	10	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	147	0	10	255	10M	=	1	-19	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r1	83	0	10	255	10M	=	1	-19	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	10	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 2 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r1	0	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r1	16	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --trim3 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	4	255	9M	*	0	0	ATCGATCAG	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --trim3 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	6	255	9M	*	0	0	CGATCAGTA	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --trim5 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	4	255	9M	*	0	0	ATCGATCAG	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug   -s 1 --trim5 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	6	255	9M	*	0	0	CGATCAGTA	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:1, sam:1)
References:
>0
TGC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:3
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	1S3M	*	0	0	ATGC	IIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
(fw:0, sam:1)
References:
>0
TGC
./bowtie2 --debug   --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:3
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	1S3M	*	0	0	ATGC	IIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug    --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug    --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug    --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug    --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
r2	0	0	1	255	1S6M	*	0	0	ATTGTTC	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
r2	16	0	1	255	1S6M	*	0	0	ATTGTTC	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r2	4	*	0	0	*	*	0	0	GTTCGTA	IIIIIII	YT:Z:UU
r3	4	*	0	0	*	*	0	0	ATTGTTC	IIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r2	4	*	0	0	*	*	0	0	TACGAAC	IIIIIII	YT:Z:UU
r3	4	*	0	0	*	*	0	0	GAACAAT	IIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -X 1000 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2 --debug   -X 1000 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2 --debug   -X 1000 --local --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2 --debug   -X 1000 --local --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2 --debug   -X 1000 --fr --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	1	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	487	1	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	1	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	724	1	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2 --debug   -X 1000 --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	487	1	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	1	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	724	1	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	1	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2 --debug   -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	1	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	487	1	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	1	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	724	1	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2 --debug   -X 1000 --local --fr --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	487	1	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	1	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	724	1	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	1	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -X 150 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   -X 150 --fr --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   --local -X 150 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   --local -X 150 --fr --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   -X 150 --fr --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   --local -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   --local -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug    --fr --quiet -M 1 -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug    --fr --quiet -M 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug    --fr --quiet -M 1 --local -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug    --fr --quiet -M 1 --local -X 150 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --fr --quiet -k 1 -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug    --fr --quiet -k 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   -X 150 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	42	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	42	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   -X 150 --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	42	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	42	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   -X 150 --local --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	44	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	44	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --debug   -X 150 --local --fr --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	44	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	44	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:2607
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	961	1	33M	=	1027	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	1027	1	28M	=	961	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA
./bowtie2 --debug   -X 150 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:2607
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	2449	1	28M	=	2383	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	2383	1	33M	=	2449	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --local -X 150 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1906
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	1672	1	33M	=	1738	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	1738	1	28M	=	1672	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC
./bowtie2 --debug   --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:1906
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	1738	1	28M	=	1672	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	1672	1	33M	=	1738	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	42	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	42	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2 --debug   --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	44	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -M w/ 1 hit local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2 --debug   --local --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	44	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2 --debug    --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2 --debug    --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2 --debug   --local --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -m w/ 1 hit local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2 --debug   --local --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug   --local --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug   --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -M 2 --local --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -M 2 --local --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -k 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -k 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug   --local --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug   --local --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -X 150 --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug   -X 150 --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug   --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug   --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	219	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	304	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug    --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	219	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug   --local --quiet -k 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	219	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	304	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --debug   --local --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	219	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
r0	256	0	1	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
r0	272	0	9	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCAT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATGAACAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2 --debug   --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
Gap penalties 1 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	6M1D6M	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	AS:i:-39	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^G6	YT:Z:UU
Gap penalties 1 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	6M1D6M	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	AS:i:-39	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^G6	YT:Z:UU
Gap penalties 2 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	YT:Z:UU
Gap penalties 2 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAAGAACAA	IIIIIIIIIIII	YT:Z:UU
Gap penalties 3 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
Gap penalties 3 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
Gap penalties 4 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 4 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAATCGAACAA	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 5 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 5 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAATCGAACAA	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 6 (fw:1, sam:1)
References:
>0
ATTGTTCGTTTGTTCGTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:18
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	6M1D5M1I6M	*	0	0	ATTGTTGTTTGATTCGTA	IIIIIIIIIIIIIIIIII	AS:i:-57	XN:i:0	XM:i:0	XO:i:2	XG:i:2	NM:i:2	MD:Z:6^C11	YT:Z:UU
Gap penalties 6 (fw:0, sam:1)
References:
>0
ATTGTTCGTTTGTTCGTA
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:18
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	6M1D5M1I6M	*	0	0	ATTGTTGTTTGATTCGTA	IIIIIIIIIIIIIIIIII	AS:i:-57	XN:i:0	XM:i:0	XO:i:2	XG:i:2	NM:i:2	MD:Z:6^C11	YT:Z:UU
Gap penalties 7 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTGTTTGATTCGT	IIIIIIIIIIIIIIII	YT:Z:UU
Gap penalties 7 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACGAATCAAACAACAA	IIIIIIIIIIIIIIII	YT:Z:UU
N filtering 1 (fw:1, sam:1)
References:
>0
GAGACTTTATACGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
N filtering 1 (fw:0, sam:1)
References:
>0
GAGACTTTATACGCATCGAACTATCGCTCTA
./bowtie2 --debug   --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
N filtering 2 (fw:1, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 2 (fw:0, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2 --debug   --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 3 (fw:1, sam:1)
References:
>0
GAGACTTTATACGCATCGAANTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 3 (fw:0, sam:1)
References:
>0
GAGACTTTATACGCATCGAANTATCGCTCTA
./bowtie2 --debug   --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 4 (fw:1, sam:1)
References:
>0
GAGACTTTNTACGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 4 (fw:0, sam:1)
References:
>0
GAGACTTTNTACGCATCGAACTATCGCTCTA
./bowtie2 --debug   --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 5 (fw:1, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:2N10	YT:Z:UU
N filtering 5 (fw:0, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2 --debug   --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:2N10	YT:Z:UU
N filtering 6 (fw:1, sam:1)
References:
>0
GAGACTTTNTACGCATCGAANTATCGCTCTA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 6 (fw:0, sam:1)
References:
>0
GAGACTTTNTACGCATCGAANTATCGCTCTA
./bowtie2 --debug   --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTTTGTTCGTTTG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	9M1I4M	*	0	0	TTTTGTTCGATTTG	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTTTGTTCGTTTG
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	9M1I4M	*	0	0	TTTTGTTCGATTTG	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTT
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCA
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	2M	*	0	0	CA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCA
./bowtie2 --debug    --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	2M	*	0	0	CA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (1) (fw:1, sam:1)
References:
>0
ACNCA
./bowtie2 --debug    --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	2M	*	0	0	AC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (1) (fw:0, sam:1)
References:
>0
ACNCA
./bowtie2 --debug    --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	2M	*	0	0	AC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (2) (fw:1, sam:1)
References:
>0
ACNCANNNNNNNNCGNNNNNNNNCG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:25
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (2) (fw:0, sam:1)
References:
>0
ACNCANNNNNNNNCGNNNNNNNNCG
./bowtie2 --debug    --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:25
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2 --debug    --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2 --debug    --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2 --debug    --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTYGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	1	255	8M	*	0	0	TTGTTGGT	IIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:5N2	YT:Z:UU
r1	0	0	1	255	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:5N2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATAACCTTCG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:10
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	4M2D4M	*	0	0	ATAATTCG	IIIIIIII	AS:i:-15	XN:i:0	XM:i:0	XO:i:1	XG:i:2	NM:i:2	MD:Z:4^CC4	YT:Z:UU
(fw:0, sam:1)
References:
>0
ATAACCTTCG
./bowtie2 --debug    --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:10
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	4M2D4M	*	0	0	ATAATTCG	IIIIIIII	AS:i:-15	XN:i:0	XM:i:0	XO:i:1	XG:i:2	NM:i:2	MD:Z:4^CC4	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATATGCCCCATGCCCCCCTCCG
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:22
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	9M3D10M	*	0	0	ATATGCCCCCCCCCCTCCG	IIIIIIIIIIIIIIIIIII	AS:i:-20	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:9^ATG10	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATATGCCCCATGCCCCCCTCCG
./bowtie2 --debug    --quiet -a --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:22
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	9M3D10M	*	0	0	ATATGCCCCCCCCCCTCCG	IIIIIIIIIIIIIIIIIII	AS:i:-20	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:9^ATG10	YT:Z:UU
Simple paired-end 13 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -I 0 -X 35 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	65	0	4	255	10M	=	30	36	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	129	0	30	255	10M	=	4	-36	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r2	67	0	4	255	10M	=	29	35	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r2	131	0	29	255	10M	=	4	-35	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	67	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	131	0	28	255	10M	=	4	-34	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r4	65	0	5	255	10M	=	31	36	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r4	129	0	31	255	10M	=	5	-36	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r5	67	0	5	255	10M	=	30	35	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r5	131	0	30	255	10M	=	5	-35	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	67	0	5	255	10M	=	29	34	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	131	0	29	255	10M	=	5	-34	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	67	0	5	255	10M	=	28	33	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	131	0	28	255	10M	=	5	-33	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 13 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2 --debug   -I 0 -X 35 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz"
r0	113	0	31	255	10M	=	4	-37	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	113	0	30	255	10M	=	4	-36	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	177	0	4	255	10M	=	30	36	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r2	115	0	29	255	10M	=	4	-35	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r2	179	0	4	255	10M	=	29	35	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	115	0	28	255	10M	=	4	-34	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	179	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r4	113	0	31	255	10M	=	5	-36	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r4	177	0	5	255	10M	=	31	36	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r5	115	0	30	255	10M	=	5	-35	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r5	179	0	5	255	10M	=	30	35	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	115	0	29	255	10M	=	5	-34	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	179	0	5	255	10M	=	29	34	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	115	0	28	255	10M	=	5	-33	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	179	0	5	255	10M	=	28	33	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 12 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -I 0 -X 36 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	GGCCCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	67	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	131	0	28	255	10M	=	4	-34	CCGGGCCCGC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 12 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC
./bowtie2 --debug   -I 0 -X 36 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	113	0	31	255	10M	=	4	-37	GGCCCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	115	0	28	255	10M	=	4	-34	CCGGGCCCGC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	179	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 11 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 11 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2 --debug   -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	31	255	10M	=	4	-37	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 10 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -I 28 -X 80 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:41
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	10M	=	21	27	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	21	255	10M	=	4	-27	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 10 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2 --debug   -I 28 -X 80 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:41
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	21	255	10M	=	4	-27	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	21	27	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 9 (fw:1, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	38	1	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	60	1	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 9 (fw:0, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2 --debug   -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	60	1	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	163	0	38	1	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 8 (fw:1, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -I 0 -X 80 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	1	10M	=	60	66	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	60	1	10M	=	4	-66	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	355	0	38	1	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	403	0	60	1	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	355	0	20	1	10M	=	60	50	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	403	0	60	1	10M	=	20	-50	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 8 (fw:0, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2 --debug   -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	60	1	10M	=	4	-66	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	163	0	4	1	10M	=	60	66	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	339	0	60	1	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	419	0	38	1	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	339	0	60	1	10M	=	20	-50	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	419	0	20	1	10M	=	60	50	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 2; no --no-mixed (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	153	0	4	255	10M	=	4	0	ATATATATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UP
r0	101	0	4	0	*	=	4	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
Simple paired-end 2; --no-mixed (fw:1, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	ATATATATAT	IIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
Simple paired-end 2; --no-mixed (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC
./bowtie2 --debug   -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	ATATATATAT	IIIIIIIIII	YT:Z:UP
Simple paired-end 1 (fw:1, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   -I 0 -X 50 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	10M	=	36	42	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	131	0	36	255	10M	=	4	-42	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 1 (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC
./bowtie2 --debug   -I 0 -X 50 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	36	255	10M	=	4	-42	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	179	0	4	255	10M	=	36	42	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:1, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2 --debug    --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug    --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug   --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --debug   --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --debug    --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug    --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy SEED=0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy SEED=0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	256	0	9	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	256	0	5	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-3	XS:i:-2	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:1C0G2T2	YT:Z:UU
r0	256	0	8	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2T0G1T0C0G0	YT:Z:UU
r0	256	0	6	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:0C0G0T2G0T1	YT:Z:UU
r0	256	0	4	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2C0G1T0T0G0	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --debug   --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	272	0	1	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	272	0	5	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-3	XS:i:-2	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:1C0G2T2	YT:Z:UU
r0	272	0	8	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2T0G1T0C0G0	YT:Z:UU
r0	272	0	4	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2C0G1T0T0G0	YT:Z:UU
r0	272	0	6	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:0C0G0T2G0T1	YT:Z:UU
FASTA-continuous 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -F 10,9 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -F 10,9 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq2_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -F 10,9 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-l --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz"
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/<<PKGBUILDDIR>>/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz"
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAG
./bowtie2-build --large-index --quiet  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -F 10,1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp  .simple_tests.gz
E: Build killed with signal TERM after 150 minutes of inactivity
--------------------------------------------------------------------------------
Build finished at 2019-12-31T11:47:20Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 158700
Build-Time: 10917
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 176
Job: bowtie2_2.3.5.1-6
Machine Architecture: armhf
Package: bowtie2
Package-Time: 11114
Source-Version: 2.3.5.1-6
Space: 158700
Status: attempted
Version: 2.3.5.1-6
--------------------------------------------------------------------------------
Finished at 2019-12-31T11:47:20Z
Build needed 03:05:14, 158700k disk space