bowtie2 →
2.3.5.1-6 →
armhf → 2020-01-17 18:31:47
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| bowtie2 2.3.5.1-6 (armhf) Wed, 15 Jan 2020 14:25:09 +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-d2358c0e-1eb2-40d9-a3da-4b2ebf5ac03d' 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]
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+------------------------------------------------------------------------------+
| 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]
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I: NOTICE: Log filtering will replace 'build/bowtie2-Wi35JV/bowtie2-2.3.5.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bowtie2-Wi35JV' 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-E9s9Gz/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-E9s9Gz/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-E9s9Gz/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-E9s9Gz/apt_archive ./ InRelease
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Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
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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-E9s9Gz/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-E9s9Gz/apt_archive ./ InRelease
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Get:3 copy:/<<BUILDDIR>>/resolver-E9s9Gz/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-E9s9Gz/apt_archive ./ Sources [553 B]
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Reading package lists...
Install bowtie2 build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
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 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
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 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, 56 newly installed, 0 to remove and 0 not upgraded.
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Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
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Get:45 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
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Get:50 http://172.17.0.1/private bullseye-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libmodule-build-perl all 0.422900-1 [258 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf liblocal-lib-perl all 2.000024-1 [53.7 kB]
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Get:55 http://172.17.0.1/private bullseye-staging/main armhf libtest-deep-perl all 1.128-1 [48.8 kB]
Get:56 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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Setting up libsigsegv2:armhf (2.12-2) ...
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Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libtbb-dev:armhf (2020.0-2) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) 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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Not building database; man-db/auto-update is not 'true'.
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Setting up dh-autoreconf (19) ...
Setting up debhelper (12.7.3) ...
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Processing triggers for libc-bin (2.29-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.1-6+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-22+rpi1 gcc-9_9.2.1-22+rpi1 libc6-dev_2.29-7+rpi1 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 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_3.5.47 bash_5.0-5 binutils_2.33.1-6+rpi1 binutils-arm-linux-gnueabihf_2.33.1-6+rpi1 binutils-common_2.33.1-6+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_9.2.1-22+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.3 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.19-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-3 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-22+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-3+b1 gcc-8-base_8.3.0-26+rpi1 gcc-9_9.2.1-22+rpi1 gcc-9-base_9.2.1-22+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.19-1 gnupg-l10n_2.2.19-1 gnupg-utils_2.2.19-1 gpg_2.2.19-1 gpg-agent_2.2.19-1 gpg-wks-client_2.2.19-1 gpg-wks-server_2.2.19-1 gpgconf_2.2.19-1 gpgsm_2.2.19-1 gpgv_2.2.19-1 grep_3.3-1 groff-base_1.22.4-4 gzip_1.9-3 help2man_1.47.12 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-22+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-22+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-6+rpi1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-7+rpi1 libc-dev-bin_2.29-7+rpi1 libc6_2.29-7+rpi1 libc6-dev_2.29-7+rpi1 libcap-ng0_0.7.9-2.1 libcc1-0_9.2.1-22+rpi1 libclone-perl_0.43-2 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.5-2 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_9.2.1-22+rpi1 libgcc1_1:9.2.1-22+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-22+rpi1 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_1:5.38-3 libmagic1_1:5.38-3 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-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_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpython3-stdlib_3.7.5-3 libpython3.7-minimal_3.7.6-1 libpython3.7-stdlib_3.7.6-1 libreadline8_8.0-3 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1+fossil191229-1 libss2_1.45.5-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 libsub-override-perl_0.09-2 libsystemd0_244-3+rpi1+b1 libtasn1-6_4.15.0-2 libtbb-dev_2020.0-2 libtbb2_2020.0-2 libtest-deep-perl_1.128-1 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-22+rpi1 libuchardet0_0.0.6-3 libudev1_244-3+rpi1+b1 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_1:4.8-1 logsave_1.45.5-2 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_6.0 passwd_1:4.8-1 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_3.7.5-3 python3-minimal_3.7.5-3 python3.7_3.7.6-1 python3.7-minimal_3.7.6-1 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 disc 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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-d2358c0e-1eb2-40d9-a3da-4b2ebf5ac03d
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
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 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, 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]
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 | };
| ^
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
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]
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 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_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);
| ^~~~~~~~
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);
| ^~~~~~~~
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 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_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 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 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_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 13 -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 13 -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 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
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 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 --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 -F 10,9 -s 1 --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-s --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 7 -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 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 -u 1 -s 1 --quiet -a --reads-per-batch 11 -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 9 -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 9 -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 1 -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 1 -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 1 -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 1 -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 1 -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 1 -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 16 -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 16 -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 11 -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 11 -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 8 -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 8 -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 11 -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
(ERR): bowtie2-align exited with value 134
Cline 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 7 -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
(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 11 -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 11 -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 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 3:12 --quiet -a --reads-per-batch 7 -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 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 --trim-to 12 --quiet -a --reads-per-batch 8 -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 3 -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 3 -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 2 -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 2 -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 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 --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 3 -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 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 --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 10 -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 4 -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 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
Cline multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 16 -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 16 -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 14 -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 14 -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 16 -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 16 -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 2 -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 2 -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 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 --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 -u 1 --quiet -a --reads-per-batch 8 -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 8 -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 15 -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 15 -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 11 -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 11 -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 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 --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
Fastq 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --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 --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 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 15 -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
(ERR): bowtie2-align exited with value 134
Fastq 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 8 -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
(ERR): bowtie2-align exited with value 134
Fastq 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 9 -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
(ERR): bowtie2-align exited with value 134
Fastq 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --trim3 4 --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 --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 3 -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 11 -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 11 -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 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 -s 1 --quiet -a --reads-per-batch 4 -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 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
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 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 -u 1 --quiet -a --reads-per-batch 14 -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 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 -u 2 --quiet -a --reads-per-batch 16 -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 6 -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 6 -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 15 -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 15 -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 10 -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 10 -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 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 --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 1 -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 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 --quiet -a --reads-per-batch 2 -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 8 -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 8 -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 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 --quiet -a --reads-per-batch 11 -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 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
(ERR): bowtie2-align exited with value 134
Fasta 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 11 -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
(ERR): bowtie2-align exited with value 134
Fasta 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --trim3 4 --quiet -a --reads-per-batch 10 -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 10 -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 8 -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 8 -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 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 -s 1 --quiet -a --reads-per-batch 2 -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 8 -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 8 -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 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 -u 1 --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
Fasta multiread 3 (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 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 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 --wrapper basic-0 -u 2 --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 multiline 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 2 --quiet -a --reads-per-batch 13 -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 13 -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 15 -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 15 -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 1 -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 1 -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 1 -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 1 -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 5 -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 5 -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 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 --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 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --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 --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 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 16 -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 16 -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 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 --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -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 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 --trim3 16 --quiet -a --reads-per-batch 12 -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 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 -s 1 --quiet -a --reads-per-batch 3 -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 16 -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 16 -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 2 -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 2 -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 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 -u 2 --quiet -a --reads-per-batch 13 -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 3 -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 3 -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 13 -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 13 -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 9 -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 9 -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 3 -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 3 -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 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 --wrapper basic-0 --quiet -a --reads-per-batch 11 -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 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 --quiet -a --reads-per-batch 12 -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 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 --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 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
(ERR): bowtie2-align exited with value 134
Tabbed 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 7 -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
(ERR): bowtie2-align exited with value 134
Tabbed 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --trim3 4 --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 --trim3 4 --quiet -a --reads-per-batch 8 -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 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 --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 6 -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 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 -s 1 --quiet -a --reads-per-batch 5 -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 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 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 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 --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -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 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 -u 2 --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 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 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 --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 -s 1 --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 -s 1 --quiet -a --reads-per-batch 5 -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 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 --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -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 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 --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 6 -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 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 --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 --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 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 7 -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 7 -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 4 -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
(ERR): bowtie2-align exited with value 134
Qseq 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --trim3 4 --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 --trim3 4 --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 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 7 -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 7 -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 7 -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 7 -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 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 --quiet -a --reads-per-batch 6 -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 15 -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 15 -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 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 --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -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 11 -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 11 -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 8 -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 8 -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 9 -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 9 -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 1 -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 1 -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 2 -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 2 -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 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 --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 --fr --quiet --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:1028
@PG ID:bowtie2 PN:bowtie2 VN:2.3.5.1 CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 3 -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 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 --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 --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:290
@PG ID:bowtie2 PN:bowtie2 VN:2.3.5.1 CL:"/<<PKGBUILDDIR>>/bowtie2-align-s --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 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 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 --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^A0C39 YT:Z:UU
MD:Z 1 (fw:0, sam:1)
References:
>0
CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2 --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:54
@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 -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 11 -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 11 -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 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 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 6 -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 6 -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 15 -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 15 -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 5 -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 5 -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 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 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 3 -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 3 -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 15 -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 15 -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 15 -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 15 -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 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;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 8 -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 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 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 7 -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 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 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 1 -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 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 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 13 -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 13 -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 13 -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 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 --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 4 -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 10 -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 10 -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 8 -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 8 -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 11 -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 11 -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 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
@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 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 = 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 16 -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 16 -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 11 -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 11 -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 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 --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 --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 --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; --no-discordant (fw:1, 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 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 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 --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 --ff --quiet -M 1 --no-discordant --no-mixed --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 --no-mixed --reads-per-batch 2 -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 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 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 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 --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 16 -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 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 --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 --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 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: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 15 -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 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 --no-overlap --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 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 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 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 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 --reads-per-batch 7 -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 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-dovetail --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-dovetail (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --no-dovetail --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 --no-dovetail --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 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 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-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 --no-contain --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 --wrapper basic-0 --no-contain --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-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --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 --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 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 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 --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 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 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: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 7 -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 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: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 3 -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 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 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 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: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 11 -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 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: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 12 -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 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: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 4 -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 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 --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 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 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: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 6 -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 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 --wrapper basic-0 --ignore-quals --mp 8 --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:-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 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 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 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: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 12 -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 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 --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 --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 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 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 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 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 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 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 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -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 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 -L 6 --mp 6,3 --score-min=C,-6 --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 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 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 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -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 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 3,3 --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 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 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 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 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 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 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 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 -L 6 --mp 6,3 --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
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 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 --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 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 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 --ignore-quals --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 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 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 --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 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 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 --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 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 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 --ignore-quals --quiet -M 1 --reads-per-batch 9 -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 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 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 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 --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 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 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 --ignore-quals --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 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 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 --ignore-quals --quiet -M 1 --reads-per-batch 12 -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 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 --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 --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: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 12 -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 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 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 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 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 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 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 --quiet -M 1 --reads-per-batch 15 -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
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 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 --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 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 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 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 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 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 3 -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 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 --quiet -M 1 --reads-per-batch 9 -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 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 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 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 --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 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --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 --seed=52 --quiet -M 1 --reads-per-batch 14 -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 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 --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 16 -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 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 --seed=53 --quiet -M 2 --reads-per-batch 4 -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 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: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 5 -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 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 --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 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --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: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 6 -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 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: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 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 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 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=0,5,C,1,1 --score-min=C,-12 --seed=55 --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 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 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: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 8 -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 16 -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 16 -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 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 --quiet -a --reads-per-batch 5 -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 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 -L 18 --quiet -a --reads-per-batch 3 -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 14 -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 14 -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 10 -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 10 -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 9 -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 9 -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 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 --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 = 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 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 --wrapper basic-0 --ff --quiet -a --reads-per-batch 14 -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 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 --rf --quiet -a --reads-per-batch 2 -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 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 --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 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 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 --wrapper basic-0 --rf --quiet -a --reads-per-batch 14 -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 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 --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 = 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 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: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 8 -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 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 --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 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 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 --fr --quiet -a --reads-per-batch 6 -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 13 -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 13 -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 5 -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 5 -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 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 --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 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 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: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 6 -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 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: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 8 -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 15 -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 15 -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 10 -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 10 -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 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 --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 -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 --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 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 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 --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -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 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 --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 -s 1 --fr --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: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 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"
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 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 --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 -s 2 --quiet -a --reads-per-batch 14 -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 14 -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 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 --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 7 -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 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 2 --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"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -s 2 --fr --quiet -a --reads-per-batch 9 -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 9 -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 8 -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 8 -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 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 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 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 --trim3 2 --quiet -a --reads-per-batch 3 -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 14 -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 14 -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 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 1 --trim5 2 --quiet -a --reads-per-batch 11 -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 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 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 1 -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 1 -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 11 -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 11 -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 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 --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 --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
@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"
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 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 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 4 -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 4 -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 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: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 2 -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 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 --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -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 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:8
@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,.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 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:8
@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,.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 11 -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 11 -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 11 -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 11 -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 15 -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 15 -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 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 --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 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --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: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 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 --overhang --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
@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 11 -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 5 -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 5 -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 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 --quiet -a --reads-per-batch 2 -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 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: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 8 -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 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: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 3 -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 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: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 10 -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 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 --local --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: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 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 --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 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 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 --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 -X 1000 --local --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 --local --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 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 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: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 1 -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 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 --wrapper basic-0 -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: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 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 -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 --local -X 150 --fr --quiet -M 2 --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 --local -X 150 --fr --quiet -M 2 --reads-per-batch 13 -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 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 --local -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: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 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 --wrapper basic-0 -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: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 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 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 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: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 6 -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 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 --local -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: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 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: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 8 -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 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 --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 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 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 --local -X 150 --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 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 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: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 15 -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 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: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 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.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 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: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 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: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 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: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 10 -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 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: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 11 -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 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 --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 -X 150 --local --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 --wrapper basic-0 -X 150 --local --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 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 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: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 1 -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 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: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 16 -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 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: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 10 -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 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: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 8 -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 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 --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 --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 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: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 16 -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 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: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 13 -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 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: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 11 -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 4 -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 4 -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 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 --quiet -k 1 --reads-per-batch 1 -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 6 -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 6 -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 16 -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 16 -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 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: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 16 -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 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 --local --quiet -M 1 --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.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --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 --wrapper basic-0 --local --quiet -M 1 --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: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 2 -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 2 -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 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 --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -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 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.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 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 --wrapper basic-0 --quiet -M 2 --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.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --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: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 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.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --quiet -M 2 --local --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 --local --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.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, 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 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 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 2 --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: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 3 -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 3 -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 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 --wrapper basic-0 --local --quiet -k 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: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 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 --local --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: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 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 --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 -X 150 --quiet -M 5 --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: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 10 -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 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: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 10 -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 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: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 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.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 8 -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 8 -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 3 -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 3 -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 5 -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 5 -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 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 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 12 -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 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 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 11 -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 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 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 11 -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 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 -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 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 4 -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 4 -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 15 -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 15 -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 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=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -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 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 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 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=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 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=30,10;RFG=25,15;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 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 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 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 4 -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 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=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -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 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=31,15;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 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 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 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 12 -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 16 -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 16 -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 3 -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 3 -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 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 --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 11 -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 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 --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 11 -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 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 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 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 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 9 -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 9 -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 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 --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 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 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 --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 3 (fw:0, sam:1)
References:
>0
GAGACTTTATACGCATCGAANTATCGCTCTA
./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 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 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 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 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 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 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 --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 3 -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 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,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 16 -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 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,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 8 -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 13 -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 13 -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 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 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 5 -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 5 -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 4 -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 4 -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 15 -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 15 -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 12 -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 12 -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 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 --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 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 8 -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 8 -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 15 -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 15 -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 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 --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: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 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: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 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 --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: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 6 -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 6 -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 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: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 5 -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 9 -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 9 -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 1 -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 1 -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 15 -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 15 -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 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 --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 -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,.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 4 -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 4 -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 4 -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 1 -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 1 -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 11 -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 11 -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 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: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 1 -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 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: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 6 -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 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: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 5 -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 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: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 11 -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 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: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 4 -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 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: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 15 -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 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: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 16 -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 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 --wrapper basic-0 -I 0 -X 50 --nofw --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 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 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 --no-mixed --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 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 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: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 2 -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 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: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 8 -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 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: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 2 -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 6 -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 6 -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 2 -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 2 -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 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 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 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 --quiet -M 1 --reads-per-batch 4 -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 10 -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 10 -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 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 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 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 --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 --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 ACTAATAA IIIIIIII YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --policy SEED=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: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 11 -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 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 SEED=0 --quiet -a --reads-per-batch 6 -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 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=3;IVAL=C,1,0;MMP=C1 --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 --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --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: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 11 -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 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 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 10 -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 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 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 10 -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 1 -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 1 -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 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-s-debug --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 --debug -F 10,9 -u 1 --quiet -a --reads-per-batch 2 -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 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
FASTA-continuous 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug -F 10,9 -s 1 --quiet -a --reads-per-batch 13 -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 13 -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 12 -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 12 -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 11 -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 11 -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 15 -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 15 -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 12 -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 12 -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 4 -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 4 -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 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-debug --wrapper basic-0 --quiet -a --reads-per-batch 8 -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 13 -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 13 -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
(ERR): bowtie2-align exited with value 134
Cline 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug --quiet -a --reads-per-batch 1 -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
(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 15 -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 15 -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 15 -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 15 -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 13 -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 13 -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 16 -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 16 -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 14 -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 14 -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 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 --trim3 4 --quiet -a --reads-per-batch 5 -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 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 --trim5 16 --quiet -a --reads-per-batch 1 -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 12 -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 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
Cline multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug --quiet -a --reads-per-batch 11 -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 11 -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 9 -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 9 -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 14 -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 14 -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 14 -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 14 -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 4 -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 4 -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 1 -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 1 -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 10 -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 10 -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 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-debug --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
Fastq 3 (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 4 (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: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Aborted
(ERR): bowtie2-align exited with value 134
Fastq 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug --quiet -a --reads-per-batch 14 -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
(ERR): bowtie2-align exited with value 134
Fastq 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug --quiet -a --reads-per-batch 7 -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
(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 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 --trim3 4 --quiet -a --reads-per-batch 4 -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 11 -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 11 -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 8 -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 8 -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 11 -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 11 -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 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-debug --wrapper basic-0 -u 1 --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
Fastq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug -u 2 --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-debug --wrapper basic-0 -u 2 --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
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 9 -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 9 -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 12 -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 12 -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 7 -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 7 -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 15 -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 15 -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 3 -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 3 -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 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-debug --wrapper basic-0 --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
Fasta 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug --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-debug --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 --debug --quiet -a --reads-per-batch 1 -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
(ERR): bowtie2-align exited with value 134
Fasta 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug --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
(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 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 4 --quiet -a --reads-per-batch 6 -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 16 -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 16 -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 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 --quiet -a --reads-per-batch 11 -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 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 1 --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
Fasta multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 10 -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 10 -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 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 -u 2 --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 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 16 -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 16 -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 1 -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 1 -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 14 -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 14 -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 14 -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 14 -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 16 -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 16 -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 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-debug --wrapper basic-0 --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
Raw 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug --quiet -a --reads-per-batch 2 -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 2 -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 14 -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 14 -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 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-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 8 -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 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 --trim3 16 --quiet -a --reads-per-batch 1 -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 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 -s 1 --quiet -a --reads-per-batch 6 -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 2 -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 2 -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 2 -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 2 -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 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 -u 2 --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
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 14 -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 14 -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 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 -s 1 --quiet -a --reads-per-batch 15 -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 11 -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 11 -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 14 -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 14 -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 13 -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 13 -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 2 -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 2 -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 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 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug --quiet -a --reads-per-batch 8 -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
(ERR): bowtie2-align exited with value 134
Tabbed 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug --quiet -a --reads-per-batch 7 -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
(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 2 -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 2 -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 13 -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 13 -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 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 -s 1 --quiet -a --reads-per-batch 10 -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 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-debug --wrapper basic-0 --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 multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug -u 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-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -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 13 -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 13 -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 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 --quiet -a --reads-per-batch 1 -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 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 -s 1 --quiet -a --reads-per-batch 10 -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 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 -u 1 --quiet -a --reads-per-batch 4 -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 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 -3 7 --quiet -a --reads-per-batch 10 -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 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 2 (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_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 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 --quiet -a --reads-per-batch 2 -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 7 -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
(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 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 --trim3 4 --quiet -a --reads-per-batch 14 -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 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 16 --quiet -a --reads-per-batch 10 -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 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 -s 1 --quiet -a --reads-per-batch 10 -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 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-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -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 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-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -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 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 -u 2 --quiet -a --reads-per-batch 12 -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 6 -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 6 -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 8 -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 8 -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 7 -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 7 -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 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 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 6 -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 6 -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 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: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 5 -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 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: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 1 -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 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: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 5 -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 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: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 1 -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 11 -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 11 -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 13 -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 13 -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 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^A0A39 YT:Z:UU
MD:Z 2 (fw:0, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./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 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 5 -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 5 -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 7 -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 7 -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 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 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 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;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 9 -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 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;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 7 -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 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 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 1 -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 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 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 4 -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 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 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 16 -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 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 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 12 -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 13 -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 13 -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 9 -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 9 -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 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-debug --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 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 15 -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 15 -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 13 -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 13 -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 15 -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 15 -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 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-debug --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 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 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-debug --wrapper basic-0 --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 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 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 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 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: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 5 -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 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 --no-discordant --reads-per-batch 9 -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 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: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 5 -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-discordant --no-mixed (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug --ff --quiet -M 1 --no-discordant --no-mixed --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-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 8 -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 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 --no-mixed --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-dovetail (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug --no-dovetail --ff --quiet -M 1 --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: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 15 -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 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 --no-dovetail --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 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 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 --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 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 --reads-per-batch 1 -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 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: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 15 -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 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 --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 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 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 -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 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 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 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 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 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 --no-dovetail --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 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 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-contain --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-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --debug --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-debug --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 --debug --no-overlap --ff --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: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 6 -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 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: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 6 -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 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: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 10 -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 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: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 10 -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 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: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 11 -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 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 --rfg 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:-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 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 --rfg 1,2 --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:-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 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 --rdg 1,2 --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:-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 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 --rdg 1,2 --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:-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 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 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 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 --mp 8 --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:-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 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 --np 4 --score-min C,-41,0 -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:-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 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 --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -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 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 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 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 --quiet -M 1 --reads-per-batch 4 -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 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 -L 6 --mp 3,3 --score-min=C,-6 --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 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 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-debug --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -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 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-debug --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -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 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 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -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 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 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 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 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 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 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 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 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -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 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-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --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 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 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 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 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 --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 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 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 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 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 --multiseed=0,7,C,1 --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 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 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 --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 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 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 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 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 --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 --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: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 14 -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 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: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 10 -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 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: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 3 -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 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: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 5 -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 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 --quiet -M 1 --reads-per-batch 10 -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
TTGTTCGTTTGTTCGT
./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 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 --quiet -M 1 --reads-per-batch 8 -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 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 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 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 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 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 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 3 -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 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 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 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 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 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 --quiet -M 1 --reads-per-batch 11 -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 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 --seed=52 --quiet -M 1 --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 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 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=52 --quiet -M 1 --reads-per-batch 1 -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 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 --seed=53 --quiet -M 2 --reads-per-batch 16 -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 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 --seed=53 --quiet -M 2 --reads-per-batch 6 -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 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-debug --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 --debug --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-debug --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 --debug --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --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: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 10 -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 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-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --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 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 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-debug --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --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 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 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=0,5,C,1,1 --score-min=C,-12 --seed=55 --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 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 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-debug --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 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 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 --quiet -a --reads-per-batch 11 -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 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 --quiet -a --reads-per-batch 11 -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 2 -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 2 -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 12 -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 12 -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 10 -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 10 -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 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 -i C,1,0 --quiet -a --reads-per-batch 7 -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 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: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 13 -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 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: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 8 -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 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 --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 = 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 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 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 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 --rf --quiet -a --reads-per-batch 14 -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 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 --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 = 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 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 --fr --quiet -a --reads-per-batch 10 -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 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 --fr --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 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 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 --fr --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 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 8 -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 8 -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 6 -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 6 -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 7 -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 7 -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 5 -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 5 -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 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: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 11 -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 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: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 10 -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 12 -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 12 -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 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-debug --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 --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 -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 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"
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 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: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 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 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 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-debug --wrapper basic-0 -s 1 --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 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 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 1 --quiet -a --reads-per-batch 4 -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 1 -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 1 -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 13 -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 13 -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 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-debug --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 1 -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 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 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 --debug -s 2 --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-debug --wrapper basic-0 -s 2 --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"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug -s 2 --fr --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: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 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"
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --debug -s 1 -u 1 --quiet -a --reads-per-batch 2 -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 2 -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 11 -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 11 -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 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-debug --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 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 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-debug --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 2 -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 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-debug --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 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 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 --trim5 2 --quiet -a --reads-per-batch 13 -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 11 -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 11 -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 14 -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 14 -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 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 --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 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 5 -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 5 -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 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 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 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-debug --wrapper basic-0 --quiet -a --reads-per-batch 14 -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 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 --overhang --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 --overhang --quiet -a --reads-per-batch 14 -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 14 -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 9 -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 9 -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 10 -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 10 -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 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-debug --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 --debug --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --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: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 10 -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 3 -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 3 -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 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 --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 --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 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 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 --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 --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 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-debug --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 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 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: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 1 -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 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: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 1 -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
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAA