Raspbian Package Auto-Building

Build log for htslib (1.9-10) on armhf

htslib → 1.9-10 → armhf → 2019-03-02 17:15:54 

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on testwandboard

+==============================================================================+
| htslib 1.9-10 (armhf)                        Sat, 02 Mar 2019 16:43:19 +0000 |
+==============================================================================+

Package: htslib
Version: 1.9-10
Source Version: 1.9-10
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-5766d4c6-b9a1-4a2f-8f30-09d6de4f0462' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
Fetched 24.4 MB in 30s (821 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'htslib' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/htslib.git
Please use:
git clone https://salsa.debian.org/med-team/htslib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1303 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main htslib 1.9-10 (dsc) [2345 B]
Get:2 http://172.17.0.1/private buster-staging/main htslib 1.9-10 (tar) [1286 kB]
Get:3 http://172.17.0.1/private buster-staging/main htslib 1.9-10 (diff) [14.9 kB]
Fetched 1303 kB in 1s (2214 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/htslib-UVlrRJ/htslib-1.9' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/htslib-UVlrRJ' 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-K9R87x/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-K9R87x/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-K9R87x/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-K9R87x/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-K9R87x/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-K9R87x/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-K9R87x/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-K9R87x/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2983 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
  libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 42 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-K9R87x/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (75.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15799 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Arch check ok (armhf included in any all)

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


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

Merged Build-Depends: debhelper (>= 11~), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev
Filtered Build-Depends: debhelper (>= 11~), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev
dpkg-deb: building package 'sbuild-build-depends-htslib-dummy' in '/<<BUILDDIR>>/resolver-K9R87x/apt_archive/sbuild-build-depends-htslib-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-htslib-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-K9R87x/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-K9R87x/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-K9R87x/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-K9R87x/apt_archive ./ Sources [540 B]
Get:5 copy:/<<BUILDDIR>>/resolver-K9R87x/apt_archive ./ Packages [622 B]
Fetched 2495 B in 1s (3643 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
  libgpg-error-l10n libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
  libcurl3-gnutls libcurl4-gnutls-dev libdeflate-dev libdeflate0 libelf1
  libfile-stripnondeterminism-perl libglib2.0-0 libicu63 liblzma-dev
  libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1
  libsigsegv2 libssh2-1 libssl-dev libtool libuchardet0 libxml2 m4 man-db
  po-debconf zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
  libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
  librtmp-dev libssh2-1-dev pkg-config liblzma-doc libssl-doc libtool-doc
  gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
  libmail-box-perl
Recommended packages:
  curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs publicsuffix libltdl-dev
  libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
  libcurl3-gnutls libcurl4-gnutls-dev libdeflate-dev libdeflate0 libelf1
  libfile-stripnondeterminism-perl libglib2.0-0 libicu63 liblzma-dev
  libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1
  libsigsegv2 libssh2-1 libssl-dev libtool libuchardet0 libxml2 m4 man-db
  po-debconf sbuild-build-depends-htslib-dummy zlib1g-dev
0 upgraded, 45 newly installed, 0 to remove and 42 not upgraded.
Need to get 21.0 MB of archives.
After this operation, 75.3 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-K9R87x/apt_archive ./ sbuild-build-depends-htslib-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-2 [1230 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-2 [242 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-2 [109 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-2 [65.1 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.1.1-1 [19.7 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.1-1 [13.0 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.176-1 [158 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.3-1 [1077 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-6 [7973 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf debhelper all 12.1 [1015 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-9 [27.7 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.36.0-2 [73.6 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.64.0-1 [291 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libcurl4-gnutls-dev armhf 7.64.0-1 [365 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libdeflate0 armhf 1.2-1 [48.4 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libdeflate-dev armhf 1.2-1 [42.0 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.1a-1 [1556 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23.1 [25.1 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 15799 files and directories currently installed.)
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Selecting previously unselected package dh-exec.
Preparing to unpack .../43-dh-exec_0.23.1_armhf.deb ...
Unpacking dh-exec (0.23.1) ...
Selecting previously unselected package sbuild-build-depends-htslib-dummy.
Preparing to unpack .../44-sbuild-build-depends-htslib-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Setting up libbz2-dev:armhf (1.0.6-9) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libnghttp2-14:armhf (1.36.0-2) ...
Setting up libicu63:armhf (63.1-6) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libdeflate0:armhf (1.2-1) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libelf1:armhf (0.176-1) ...
Setting up libssl-dev:armhf (1.1.1a-1) ...
Setting up libglib2.0-0:armhf (2.58.3-1) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-9) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up m4 (1.4.18-2) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libmagic-mgc (1:5.35-2) ...
Setting up libmagic1:armhf (1:5.35-2) ...
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up libssh2-1:armhf (1.8.0-2) ...
Processing triggers for libc-bin (2.28-6+rpi1) ...
Setting up dwz (0.12-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up bsdmainutils (11.1.2) ...
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
Setting up libdeflate-dev:armhf (1.2-1) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (1.1.1-1) ...
Setting up gettext (0.19.8.1-9) ...
Setting up libcurl3-gnutls:armhf (7.64.0-1) ...
Setting up groff-base (1.22.4-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.35-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up libcurl4-gnutls-dev:armhf (7.64.0-1) ...
Setting up libtool (2.4.6-9) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.1.1-1) ...
Setting up debhelper (12.1) ...
Setting up dh-exec (0.23.1) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-6+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-20+rpi1 gcc-8_8.2.0-20+rpi1 libc6-dev_2.28-6+rpi1 libstdc++-8-dev_8.2.0-20+rpi1 libstdc++6_8.2.0-20+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~rc3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.46 bash_5.0-2 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20190110 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-20+rpi1 dash_0.5.10.2-5 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.70 debhelper_12.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-exec_0.23.1 dh-strip-nondeterminism_1.1.1-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-2 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-20+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-20+rpi1 gcc-8-base_8.2.0-20+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.133 initramfs-tools-core_0.133 intltool-debian_0.35.0+20060710.5 klibc-utils_2.0.6-1+rpi1 kmod_26-1 krb5-locales_1.17-1 libacl1_2.2.52-3 libapparmor1_2.13.2-7 libapt-pkg5.0_1.8.0~rc3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.2 libasan5_8.2.0-20+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-20+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblkid1_2.33.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.28-6+rpi1 libc-dev-bin_2.28-6+rpi1 libc6_2.28-6+rpi1 libc6-dev_2.28-6+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_8.2.0-20+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.1.0-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.64.0-1 libcurl4-gnutls-dev_7.64.0-1 libdb5.3_5.3.28+dfsg1-0.3 libdbus-1-3_1.12.12-1 libdebconfclient0_0.247 libdeflate-dev_1.2-1 libdeflate0_1.2-1 libdevmapper1.02.1_2:1.02.155-2 libdpkg-perl_1.19.2 libdrm-common_2.4.97-1+rpi1 libdrm2_2.4.97-1+rpi1 libelf1_0.176-1 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.1-1 libgcc-8-dev_8.2.0-20+rpi1 libgcc1_1:8.2.0-20+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-2 libgomp1_8.2.0-20+rpi1 libgpg-error-l10n_1.35-1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-1 libhogweed4_3.4.1-1 libicu63_63.1-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1+ds-2 libk5crypto3_1.17-1 libkeyutils1_1.6-2 libklibc_2.0.6-1+rpi1 libkmod2_26-1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses5_6.1+20181013-2 libncurses6_6.1+20181013-2 libncursesw5_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnghttp2-14_1.36.0-2 libnpth0_1.6-1 libnss-systemd_240-5+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam-systemd_240-5+rpi1 libpam0g_1.1.8-4 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-4 libperl5.28_5.28.1-4 libpipeline1_1.5.1-2 libplymouth4_0.9.4-1 libpng16-16_1.6.36-5 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.26.0+fossilbc891ac6b-2 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl-dev_1.1.1a-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-20+rpi1 libstdc++6_8.2.0-20+rpi1 libsystemd0_240-5+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-2 libtinfo6_6.1+20181013-2 libtool_2.4.6-9 libubsan1_8.2.0-20+rpi1 libuchardet0_0.0.6-3 libudev1_240-5+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-2 mawk_1.3.3-17 mount_2.33.1-0.1 multiarch-support_2.28-6+rpi1 nano_3.2-1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-4 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-5+rpi1 systemd-sysv_240-5+rpi1 sysvinit-utils_2.93-6 tar_1.30+dfsg-5 tzdata_2018i-1 udev_240-5+rpi1 util-linux_2.33.1-0.1 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 Jan 16 13:40:59 2019 UTC
gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./htslib_1.9-10.dsc
dpkg-source: info: extracting htslib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking htslib_1.9.orig.tar.gz
dpkg-source: info: unpacking htslib_1.9-10.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying no_git_version
dpkg-source: info: applying define_PATH_MAX.patch
dpkg-source: info: applying fPIC.patch
dpkg-source: info: applying testShebang.patch
dpkg-source: info: applying fix_float_precision

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-5766d4c6-b9a1-4a2f-8f30-09d6de4f0462
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd

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

dpkg-buildpackage: info: source package htslib
dpkg-buildpackage: info: source version 1.9-10
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from htslib-1.9/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$
 fakeroot debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
	make -j4 distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.tmp test/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL*
rm -f libhts.so libhts.so.*
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f libhts.a bgzip htsfile tabix  test/hts_endian test/fieldarith test/hfile test/sam test/test_bgzf test/test_realn test/test-regidx test/test_view test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/test-bcf-translate test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk
rm -rf autom4te.cache
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -rf test_backup/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/libhts2.substvars debian/libhts-dev.substvars debian/libhts-private-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files
	rm -fr -- debian/libhts2/ debian/tmp/ debian/libhts-dev/ debian/libhts-private-dev/ debian/htslib-test/ debian/tabix/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
 debian/rules build-arch
dh build-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
	find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a  -type f -exec md5sum {} + -o -type l -printf "symlink  %p
" > debian/autoreconf.before
	grep -q ^XDT_ configure.ac
	autoreconf -f -i
	find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a  -type f -exec md5sum {} + -o -type l -printf "symlink  %p
" > debian/autoreconf.after
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# create clean copy of test dir
cp -a test test_backup
autoconf
dh_auto_configure -- --enable-libcurl --enable-gcs --enable-s3
	./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for libdeflate.h... yes
checking for libdeflate_deflate_compress in -ldeflate... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
	rm -f debian/libhts-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- \
  CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
  CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
  LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
  PACKAGE_VERSION="1.9-10" \
  libdir=/usr/lib/arm-linux-gnueabihf
	make -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto" PACKAGE_VERSION=1.9-10 libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9-10"' > version.h
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_libcurl.o hfile_libcurl.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_gcs.o hfile_gcs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_s3.o hfile_s3.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o knetfile.pico knetfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_net.pico hfile_net.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/files.pico cram/files.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
gcc -shared -Wl,-soname,libhts.so.2 -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/hts_endian test/hts_endian.o -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o  hfile_libcurl.o hfile_gcs.o hfile_s3.o
ranlib libhts.a
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
ln -sf libhts.so libhts.so.2
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test -a
	make -j4 test VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo '#define HTS_VERSION "1.9"' > version.h
gcc -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o  hfile_libcurl.o hfile_gcs.o hfile_s3.o
ranlib libhts.a
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
test/hts_endian
test/fieldarith test/fieldarith.sam
test/hfile
test/test_bgzf test/bgziptest.txt
cd test/tabix && ./test-tabix.sh tabix.tst
Testing tabix...
PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz
PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero)
PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz
PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647
PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz
PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200
PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz
PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190

Expected   passes:   13
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq
test/test-regidx
cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-}
test_view testing auxf#values.sam, ref auxf.fa:
  ./test_view  -S -b auxf#values.sam > auxf#values.tmp.bam
  ./test_view  auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
  ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
  ./test_view  -S -l0 -b auxf#values.sam > auxf#values.tmp.bam
  ./test_view  auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
  ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
  ./test_view  -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram
  ./test_view  -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view  -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
  ./test_view  -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
  ./test_view  auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
  ./test_view  -t auxf.fa -S -l0 -C -o VERSION=3.0 auxf#values.sam > auxf#values.tmp.cram
  ./test_view  -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view  -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
  ./test_view  -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
  ./test_view  auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
  ./test_view  -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
  ./test_view  -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
  ./test_view  -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
  ./test_view  auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view  -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_
  ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_
.. ok

test_view testing c1#bounds.sam, ref c1.fa:
  ./test_view  -S -b c1#bounds.sam > c1#bounds.tmp.bam
  ./test_view  c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
  ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
  ./test_view  -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam
  ./test_view  c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
  ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram
  ./test_view  -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
  ./test_view  -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
  ./test_view  c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -S -l0 -C -o VERSION=3.0 c1#bounds.sam > c1#bounds.tmp.cram
  ./test_view  -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
  ./test_view  -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
  ./test_view  c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
  ./test_view  c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
.. ok

test_view testing c1#clip.sam, ref c1.fa:
  ./test_view  -S -b c1#clip.sam > c1#clip.tmp.bam
  ./test_view  c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
  ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
  ./test_view  -S -l0 -b c1#clip.sam > c1#clip.tmp.bam
  ./test_view  c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
  ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram
  ./test_view  -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
  ./test_view  -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
  ./test_view  c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -S -l0 -C -o VERSION=3.0 c1#clip.sam > c1#clip.tmp.cram
  ./test_view  -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
  ./test_view  -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
  ./test_view  c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
  ./test_view  c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
.. ok

test_view testing c1#noseq.sam, ref c1.fa:
  ./test_view  -S -b c1#noseq.sam > c1#noseq.tmp.bam
  ./test_view  c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
  ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
  ./test_view  -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam
  ./test_view  c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
  ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram
  ./test_view  -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
  ./test_view  -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
  ./test_view  c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -S -l0 -C -o VERSION=3.0 c1#noseq.sam > c1#noseq.tmp.cram
  ./test_view  -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
  ./test_view  -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
  ./test_view  c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
  ./test_view  c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
.. ok

test_view testing c1#pad1.sam, ref c1.fa:
  ./test_view  -S -b c1#pad1.sam > c1#pad1.tmp.bam
  ./test_view  c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
  ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
  ./test_view  -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam
  ./test_view  c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
  ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram
  ./test_view  -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
  ./test_view  -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
  ./test_view  c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad1.sam > c1#pad1.tmp.cram
  ./test_view  -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
  ./test_view  -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
  ./test_view  c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
  ./test_view  c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
.. ok

test_view testing c1#pad2.sam, ref c1.fa:
  ./test_view  -S -b c1#pad2.sam > c1#pad2.tmp.bam
  ./test_view  c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
  ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
  ./test_view  -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam
  ./test_view  c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
  ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram
  ./test_view  -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
  ./test_view  -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
  ./test_view  c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad2.sam > c1#pad2.tmp.cram
  ./test_view  -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
  ./test_view  -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
  ./test_view  c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
  ./test_view  c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
.. ok

test_view testing c1#pad3.sam, ref c1.fa:
  ./test_view  -S -b c1#pad3.sam > c1#pad3.tmp.bam
  ./test_view  c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
  ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
  ./test_view  -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam
  ./test_view  c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
  ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram
  ./test_view  -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
  ./test_view  -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
  ./test_view  c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad3.sam > c1#pad3.tmp.cram
  ./test_view  -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
  ./test_view  -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
  ./test_view  c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
  ./test_view  c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
.. ok

test_view testing c1#unknown.sam, ref c1.fa:
  ./test_view  -S -b c1#unknown.sam > c1#unknown.tmp.bam
  ./test_view  c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
  ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
  ./test_view  -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam
  ./test_view  c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
  ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram
  ./test_view  -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
  ./test_view  -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
  ./test_view  c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -S -l0 -C -o VERSION=3.0 c1#unknown.sam > c1#unknown.tmp.cram
  ./test_view  -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
  ./test_view  -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
  ./test_view  c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
  ./test_view  -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
  ./test_view  -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
  ./test_view  c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
.. ok

test_view testing c2#pad.sam, ref c2.fa:
  ./test_view  -S -b c2#pad.sam > c2#pad.tmp.bam
  ./test_view  c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
  ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
  ./test_view  -S -l0 -b c2#pad.sam > c2#pad.tmp.bam
  ./test_view  c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
  ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
  ./test_view  -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram
  ./test_view  -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
  ./test_view  -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
  ./test_view  -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
  ./test_view  c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
  ./test_view  -t c2.fa -S -l0 -C -o VERSION=3.0 c2#pad.sam > c2#pad.tmp.cram
  ./test_view  -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
  ./test_view  -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
  ./test_view  -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
  ./test_view  c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
  ./test_view  -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
  ./test_view  -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
  ./test_view  -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
  ./test_view  c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
.. ok

test_view testing ce#1.sam, ref ce.fa:
  ./test_view  -S -b ce#1.sam > ce#1.tmp.bam
  ./test_view  ce#1.tmp.bam > ce#1.tmp.bam.sam_
  ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#1.sam > ce#1.tmp.bam
  ./test_view  ce#1.tmp.bam > ce#1.tmp.bam.sam_
  ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram
  ./test_view  -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#1.tmp.bam > ce#1.tmp.bam.cram
  ./test_view  -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
  ./test_view  ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1.sam > ce#1.tmp.cram
  ./test_view  -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
  ./test_view  -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
  ./test_view  ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
  ./test_view  ce#1.tmp.cram > ce#1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
.. ok

test_view testing ce#1000.sam, ref ce.fa:
  ./test_view  -S -b ce#1000.sam > ce#1000.tmp.bam
  ./test_view  ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
  ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#1000.sam > ce#1000.tmp.bam
  ./test_view  ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
  ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram
  ./test_view  -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
  ./test_view  -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
  ./test_view  ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram
  ./test_view  -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
  ./test_view  -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
  ./test_view  ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
  ./test_view  ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
.. ok

test_view testing ce#2.sam, ref ce.fa:
  ./test_view  -S -b ce#2.sam > ce#2.tmp.bam
  ./test_view  ce#2.tmp.bam > ce#2.tmp.bam.sam_
  ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#2.sam > ce#2.tmp.bam
  ./test_view  ce#2.tmp.bam > ce#2.tmp.bam.sam_
  ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram
  ./test_view  -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#2.tmp.bam > ce#2.tmp.bam.cram
  ./test_view  -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
  ./test_view  ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#2.sam > ce#2.tmp.cram
  ./test_view  -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
  ./test_view  -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
  ./test_view  ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
  ./test_view  ce#2.tmp.cram > ce#2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
.. ok

test_view testing ce#5.sam, ref ce.fa:
  ./test_view  -S -b ce#5.sam > ce#5.tmp.bam
  ./test_view  ce#5.tmp.bam > ce#5.tmp.bam.sam_
  ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#5.sam > ce#5.tmp.bam
  ./test_view  ce#5.tmp.bam > ce#5.tmp.bam.sam_
  ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram
  ./test_view  -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#5.tmp.bam > ce#5.tmp.bam.cram
  ./test_view  -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
  ./test_view  ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5.sam > ce#5.tmp.cram
  ./test_view  -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
  ./test_view  -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
  ./test_view  ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
  ./test_view  ce#5.tmp.cram > ce#5.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
.. ok

test_view testing ce#5b.sam, ref ce.fa:
  ./test_view  -S -b ce#5b.sam > ce#5b.tmp.bam
  ./test_view  ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
  ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#5b.sam > ce#5b.tmp.bam
  ./test_view  ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
  ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram
  ./test_view  -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
  ./test_view  -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
  ./test_view  ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5b.sam > ce#5b.tmp.cram
  ./test_view  -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
  ./test_view  -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
  ./test_view  ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
  ./test_view  ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
  ./test_view  -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_
  ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_
.. ok

test_view testing ce#large_seq.sam, ref ce.fa:
  ./test_view  -S -b ce#large_seq.sam > ce#large_seq.tmp.bam
  ./test_view  ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
  ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam
  ./test_view  ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
  ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram
  ./test_view  -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
  ./test_view  -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
  ./test_view  ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#large_seq.sam > ce#large_seq.tmp.cram
  ./test_view  -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
  ./test_view  -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
  ./test_view  ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
  ./test_view  ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
.. ok

test_view testing ce#supp.sam, ref ce.fa:
  ./test_view  -S -b ce#supp.sam > ce#supp.tmp.bam
  ./test_view  ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
  ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#supp.sam > ce#supp.tmp.bam
  ./test_view  ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
  ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram
  ./test_view  -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
  ./test_view  -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
  ./test_view  ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#supp.sam > ce#supp.tmp.cram
  ./test_view  -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
  ./test_view  -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
  ./test_view  ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
  ./test_view  ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
.. ok

test_view testing ce#tag_depadded.sam, ref ce.fa:
  ./test_view  -S -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
  ./test_view  ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
  ./test_view  ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
  ./test_view  -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
  ./test_view  -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
  ./test_view  ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
  ./test_view  -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
  ./test_view  -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
  ./test_view  ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
  ./test_view  ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
.. ok

test_view testing ce#tag_padded.sam, ref ce.fa:
  ./test_view  -S -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
  ./test_view  ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
  ./test_view  ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram
  ./test_view  -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
  ./test_view  -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
  ./test_view  ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_padded.sam > ce#tag_padded.tmp.cram
  ./test_view  -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
  ./test_view  -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
  ./test_view  ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
  ./test_view  ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
.. ok

test_view testing ce#unmap.sam, ref ce.fa:
  ./test_view  -S -b ce#unmap.sam > ce#unmap.tmp.bam
  ./test_view  ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
  ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam
  ./test_view  ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
  ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram
  ./test_view  -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
  ./test_view  -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
  ./test_view  ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap.sam > ce#unmap.tmp.cram
  ./test_view  -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
  ./test_view  -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
  ./test_view  ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
  ./test_view  ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
.. ok

test_view testing ce#unmap1.sam, ref ce.fa:
  ./test_view  -S -b ce#unmap1.sam > ce#unmap1.tmp.bam
  ./test_view  ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
  ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam
  ./test_view  ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
  ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram
  ./test_view  -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
  ./test_view  -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
  ./test_view  ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap1.sam > ce#unmap1.tmp.cram
  ./test_view  -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
  ./test_view  -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
  ./test_view  ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
  ./test_view  ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
.. ok

test_view testing ce#unmap2.sam, ref ce.fa:
  ./test_view  -S -b ce#unmap2.sam > ce#unmap2.tmp.bam
  ./test_view  ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
  ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam
  ./test_view  ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
  ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram
  ./test_view  -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
  ./test_view  -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
  ./test_view  ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap2.sam > ce#unmap2.tmp.cram
  ./test_view  -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
  ./test_view  -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
  ./test_view  ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
  ./test_view  -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
  ./test_view  -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
  ./test_view  ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
.. ok

test_view testing md#1.sam, ref md.fa:
  ./test_view  -S -b md#1.sam > md#1.tmp.bam
  ./test_view  md#1.tmp.bam > md#1.tmp.bam.sam_
  ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
  ./test_view  -S -l0 -b md#1.sam > md#1.tmp.bam
  ./test_view  md#1.tmp.bam > md#1.tmp.bam.sam_
  ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
  ./test_view  -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram
  ./test_view  -D md#1.tmp.cram > md#1.tmp.cram.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.cram.sam_
  ./test_view  -t md.fa -C -o VERSION=2.1 md#1.tmp.bam > md#1.tmp.bam.cram
  ./test_view  -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
  ./test_view  md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.bam.cram.bam.sam_
  ./test_view  -t md.fa -S -l0 -C -o VERSION=3.0 md#1.sam > md#1.tmp.cram
  ./test_view  -D md#1.tmp.cram > md#1.tmp.cram.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.cram.sam_
  ./test_view  -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram
  ./test_view  -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
  ./test_view  md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.bam.cram.bam.sam_
  ./test_view  -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram
  ./test_view  -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram
  ./test_view  -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
  ./test_view  md#1.tmp.cram > md#1.tmp.cram.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.cram.sam_
.. ok

test_view testing xx#blank.sam, ref xx.fa:
  ./test_view  -S -b xx#blank.sam > xx#blank.tmp.bam
  ./test_view  xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
  ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#blank.sam > xx#blank.tmp.bam
  ./test_view  xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
  ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram
  ./test_view  -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
  ./test_view  -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
  ./test_view  xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#blank.sam > xx#blank.tmp.cram
  ./test_view  -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
  ./test_view  -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
  ./test_view  xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
  ./test_view  xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
.. ok

test_view testing xx#large_aux.sam, ref xx.fa:
  ./test_view  -S -b xx#large_aux.sam > xx#large_aux.tmp.bam
  ./test_view  xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam
  ./test_view  xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram
  ./test_view  -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
  ./test_view  -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
  ./test_view  xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux.sam > xx#large_aux.tmp.cram
  ./test_view  -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
  ./test_view  -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
  ./test_view  xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
  ./test_view  xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view  -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20
  ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_
.. ok

test_view testing xx#large_aux2.sam, ref xx.fa:
  ./test_view  -S -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
  ./test_view  xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
  ./test_view  xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram
  ./test_view  -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
  ./test_view  -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
  ./test_view  xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux2.sam > xx#large_aux2.tmp.cram
  ./test_view  -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
  ./test_view  -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
  ./test_view  xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
  ./test_view  xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
.. ok

test_view testing xx#minimal.sam, ref xx.fa:
  ./test_view  -S -b xx#minimal.sam > xx#minimal.tmp.bam
  ./test_view  xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
  ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam
  ./test_view  xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
  ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram
  ./test_view  -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
  ./test_view  -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
  ./test_view  xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#minimal.sam > xx#minimal.tmp.cram
  ./test_view  -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
  ./test_view  -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
  ./test_view  xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
  ./test_view  xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
.. ok

test_view testing xx#pair.sam, ref xx.fa:
  ./test_view  -S -b xx#pair.sam > xx#pair.tmp.bam
  ./test_view  xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
  ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#pair.sam > xx#pair.tmp.bam
  ./test_view  xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
  ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram
  ./test_view  -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
  ./test_view  -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
  ./test_view  xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#pair.sam > xx#pair.tmp.cram
  ./test_view  -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
  ./test_view  -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
  ./test_view  xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
  ./test_view  xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
.. ok

test_view testing xx#repeated.sam, ref xx.fa:
  ./test_view  -S -b xx#repeated.sam > xx#repeated.tmp.bam
  ./test_view  xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
  ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam
  ./test_view  xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
  ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram
  ./test_view  -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
  ./test_view  -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
  ./test_view  xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#repeated.sam > xx#repeated.tmp.cram
  ./test_view  -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
  ./test_view  -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
  ./test_view  xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
  ./test_view  xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
.. ok

test_view testing xx#rg.sam, ref xx.fa:
  ./test_view  -S -b xx#rg.sam > xx#rg.tmp.bam
  ./test_view  xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
  ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#rg.sam > xx#rg.tmp.bam
  ./test_view  xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
  ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram
  ./test_view  -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
  ./test_view  -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
  ./test_view  xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#rg.sam > xx#rg.tmp.cram
  ./test_view  -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
  ./test_view  -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
  ./test_view  xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
  ./test_view  xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
.. ok

test_view testing xx#tlen.sam, ref xx.fa:
  ./test_view  -S -b xx#tlen.sam > xx#tlen.tmp.bam
  ./test_view  xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
  ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam
  ./test_view  xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
  ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram
  ./test_view  -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
  ./test_view  -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
  ./test_view  xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen.sam > xx#tlen.tmp.cram
  ./test_view  -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
  ./test_view  -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
  ./test_view  xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
  ./test_view  xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
.. ok

test_view testing xx#tlen2.sam, ref xx.fa:
  ./test_view  -S -b xx#tlen2.sam > xx#tlen2.tmp.bam
  ./test_view  xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
  ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam
  ./test_view  xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
  ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram
  ./test_view  -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
  ./test_view  -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
  ./test_view  xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen2.sam > xx#tlen2.tmp.cram
  ./test_view  -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
  ./test_view  -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
  ./test_view  xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
  ./test_view  xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
.. ok

test_view testing xx#triplet.sam, ref xx.fa:
  ./test_view  -S -b xx#triplet.sam > xx#triplet.tmp.bam
  ./test_view  xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
  ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam
  ./test_view  xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
  ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram
  ./test_view  -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
  ./test_view  -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
  ./test_view  xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#triplet.sam > xx#triplet.tmp.cram
  ./test_view  -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
  ./test_view  -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
  ./test_view  xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
  ./test_view  xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
.. ok

test_view testing xx#unsorted.sam, ref xx.fa:
  ./test_view  -S -b xx#unsorted.sam > xx#unsorted.tmp.bam
  ./test_view  xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
  ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam
  ./test_view  xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
  ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram
  ./test_view  -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
  ./test_view  -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
  ./test_view  xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#unsorted.sam > xx#unsorted.tmp.cram
  ./test_view  -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
  ./test_view  -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
  ./test_view  xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
  ./test_view  xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok

  ./test_view  -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
  ./test_view  range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
test_view testing auxf#values.sam, ref auxf.fa:
  ./test_view -@4 -S -b auxf#values.sam > auxf#values.tmp.bam
  ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
  ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam
  ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
  ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
  ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram
  ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view -@4 -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
  ./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
  ./test_view -@4 auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t auxf.fa -S -l0 -C -o VERSION=3.0 auxf#values.sam > auxf#values.tmp.cram
  ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
  ./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
  ./test_view -@4 auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
  ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
  ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
  ./test_view -@4 auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_
  ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_
.. ok

test_view testing c1#bounds.sam, ref c1.fa:
  ./test_view -@4 -S -b c1#bounds.sam > c1#bounds.tmp.bam
  ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
  ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam
  ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
  ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram
  ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
  ./test_view -@4 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
  ./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#bounds.sam > c1#bounds.tmp.cram
  ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
  ./test_view -@4 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
  ./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
  ./test_view -@4 c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
.. ok

test_view testing c1#clip.sam, ref c1.fa:
  ./test_view -@4 -S -b c1#clip.sam > c1#clip.tmp.bam
  ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
  ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam
  ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
  ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram
  ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
  ./test_view -@4 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
  ./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#clip.sam > c1#clip.tmp.cram
  ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
  ./test_view -@4 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
  ./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
  ./test_view -@4 c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
.. ok

test_view testing c1#noseq.sam, ref c1.fa:
  ./test_view -@4 -S -b c1#noseq.sam > c1#noseq.tmp.bam
  ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
  ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam
  ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
  ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram
  ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
  ./test_view -@4 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
  ./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#noseq.sam > c1#noseq.tmp.cram
  ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
  ./test_view -@4 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
  ./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
  ./test_view -@4 c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
.. ok

test_view testing c1#pad1.sam, ref c1.fa:
  ./test_view -@4 -S -b c1#pad1.sam > c1#pad1.tmp.bam
  ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
  ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam
  ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
  ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram
  ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
  ./test_view -@4 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
  ./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad1.sam > c1#pad1.tmp.cram
  ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
  ./test_view -@4 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
  ./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
  ./test_view -@4 c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
.. ok

test_view testing c1#pad2.sam, ref c1.fa:
  ./test_view -@4 -S -b c1#pad2.sam > c1#pad2.tmp.bam
  ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
  ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam
  ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
  ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram
  ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
  ./test_view -@4 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
  ./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad2.sam > c1#pad2.tmp.cram
  ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
  ./test_view -@4 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
  ./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
  ./test_view -@4 c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
.. ok

test_view testing c1#pad3.sam, ref c1.fa:
  ./test_view -@4 -S -b c1#pad3.sam > c1#pad3.tmp.bam
  ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
  ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam
  ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
  ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram
  ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
  ./test_view -@4 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
  ./test_view -@4 c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad3.sam > c1#pad3.tmp.cram
  ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
  ./test_view -@4 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
  ./test_view -@4 c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
  ./test_view -@4 c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
.. ok

test_view testing c1#unknown.sam, ref c1.fa:
  ./test_view -@4 -S -b c1#unknown.sam > c1#unknown.tmp.bam
  ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
  ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam
  ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
  ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram
  ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
  ./test_view -@4 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
  ./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#unknown.sam > c1#unknown.tmp.cram
  ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
  ./test_view -@4 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
  ./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
  ./test_view -@4 c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
.. ok

test_view testing c2#pad.sam, ref c2.fa:
  ./test_view -@4 -S -b c2#pad.sam > c2#pad.tmp.bam
  ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
  ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam
  ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
  ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
  ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram
  ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
  ./test_view -@4 -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
  ./test_view -@4 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
  ./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c2.fa -S -l0 -C -o VERSION=3.0 c2#pad.sam > c2#pad.tmp.cram
  ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
  ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
  ./test_view -@4 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
  ./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
  ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
  ./test_view -@4 -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
  ./test_view -@4 c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
.. ok

test_view testing ce#1.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#1.sam > ce#1.tmp.bam
  ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_
  ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam
  ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_
  ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram
  ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1.tmp.bam > ce#1.tmp.bam.cram
  ./test_view -@4 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
  ./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1.sam > ce#1.tmp.cram
  ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
  ./test_view -@4 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
  ./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
  ./test_view -@4 ce#1.tmp.cram > ce#1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
.. ok

test_view testing ce#1000.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam
  ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
  ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam
  ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
  ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram
  ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
  ./test_view -@4 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
  ./test_view -@4 ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram
  ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
  ./test_view -@4 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
  ./test_view -@4 ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
  ./test_view -@4 ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
.. ok

test_view testing ce#2.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#2.sam > ce#2.tmp.bam
  ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_
  ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam
  ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_
  ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram
  ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#2.tmp.bam > ce#2.tmp.bam.cram
  ./test_view -@4 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
  ./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#2.sam > ce#2.tmp.cram
  ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
  ./test_view -@4 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
  ./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
  ./test_view -@4 ce#2.tmp.cram > ce#2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
.. ok

test_view testing ce#5.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#5.sam > ce#5.tmp.bam
  ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_
  ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam
  ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_
  ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram
  ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5.tmp.bam > ce#5.tmp.bam.cram
  ./test_view -@4 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
  ./test_view -@4 ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5.sam > ce#5.tmp.cram
  ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
  ./test_view -@4 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
  ./test_view -@4 ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
  ./test_view -@4 ce#5.tmp.cram > ce#5.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
.. ok

test_view testing ce#5b.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#5b.sam > ce#5b.tmp.bam
  ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
  ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam
  ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
  ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram
  ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
  ./test_view -@4 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
  ./test_view -@4 ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5b.sam > ce#5b.tmp.cram
  ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
  ./test_view -@4 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
  ./test_view -@4 ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
  ./test_view -@4 ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
  ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_
  ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_
.. ok

test_view testing ce#large_seq.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#large_seq.sam > ce#large_seq.tmp.bam
  ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
  ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam
  ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
  ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram
  ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
  ./test_view -@4 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
  ./test_view -@4 ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#large_seq.sam > ce#large_seq.tmp.cram
  ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
  ./test_view -@4 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
  ./test_view -@4 ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
  ./test_view -@4 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
.. ok

test_view testing ce#supp.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#supp.sam > ce#supp.tmp.bam
  ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
  ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam
  ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
  ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram
  ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
  ./test_view -@4 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
  ./test_view -@4 ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#supp.sam > ce#supp.tmp.cram
  ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
  ./test_view -@4 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
  ./test_view -@4 ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
  ./test_view -@4 ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
.. ok

test_view testing ce#tag_depadded.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
  ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
  ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
  ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
  ./test_view -@4 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
  ./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
  ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
  ./test_view -@4 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
  ./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
  ./test_view -@4 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
.. ok

test_view testing ce#tag_padded.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
  ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
  ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram
  ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
  ./test_view -@4 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
  ./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_padded.sam > ce#tag_padded.tmp.cram
  ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
  ./test_view -@4 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
  ./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
  ./test_view -@4 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
.. ok

test_view testing ce#unmap.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#unmap.sam > ce#unmap.tmp.bam
  ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
  ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam
  ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
  ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram
  ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
  ./test_view -@4 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
  ./test_view -@4 ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap.sam > ce#unmap.tmp.cram
  ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
  ./test_view -@4 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
  ./test_view -@4 ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
  ./test_view -@4 ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
.. ok

test_view testing ce#unmap1.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#unmap1.sam > ce#unmap1.tmp.bam
  ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
  ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam
  ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
  ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram
  ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
  ./test_view -@4 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
  ./test_view -@4 ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap1.sam > ce#unmap1.tmp.cram
  ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
  ./test_view -@4 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
  ./test_view -@4 ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
  ./test_view -@4 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
.. ok

test_view testing ce#unmap2.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#unmap2.sam > ce#unmap2.tmp.bam
  ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
  ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam
  ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
  ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram
  ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
  ./test_view -@4 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
  ./test_view -@4 ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap2.sam > ce#unmap2.tmp.cram
  ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
  ./test_view -@4 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
  ./test_view -@4 ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
  ./test_view -@4 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
.. ok

test_view testing md#1.sam, ref md.fa:
  ./test_view -@4 -S -b md#1.sam > md#1.tmp.bam
  ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_
  ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam
  ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_
  ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
  ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram
  ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.cram.sam_
  ./test_view -@4 -t md.fa -C -o VERSION=2.1 md#1.tmp.bam > md#1.tmp.bam.cram
  ./test_view -@4 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
  ./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t md.fa -S -l0 -C -o VERSION=3.0 md#1.sam > md#1.tmp.cram
  ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.cram.sam_
  ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram
  ./test_view -@4 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
  ./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram
  ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram
  ./test_view -@4 -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
  ./test_view -@4 md#1.tmp.cram > md#1.tmp.cram.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.cram.sam_
.. ok

test_view testing xx#blank.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#blank.sam > xx#blank.tmp.bam
  ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
  ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam
  ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
  ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram
  ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
  ./test_view -@4 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
  ./test_view -@4 xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#blank.sam > xx#blank.tmp.cram
  ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
  ./test_view -@4 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
  ./test_view -@4 xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
  ./test_view -@4 xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
.. ok

test_view testing xx#large_aux.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#large_aux.sam > xx#large_aux.tmp.bam
  ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam
  ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram
  ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
  ./test_view -@4 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
  ./test_view -@4 xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux.sam > xx#large_aux.tmp.cram
  ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
  ./test_view -@4 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
  ./test_view -@4 xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
  ./test_view -@4 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20
  ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_
.. ok

test_view testing xx#large_aux2.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
  ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
  ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram
  ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
  ./test_view -@4 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
  ./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux2.sam > xx#large_aux2.tmp.cram
  ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
  ./test_view -@4 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
  ./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
  ./test_view -@4 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
.. ok

test_view testing xx#minimal.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#minimal.sam > xx#minimal.tmp.bam
  ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
  ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam
  ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
  ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram
  ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
  ./test_view -@4 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
  ./test_view -@4 xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#minimal.sam > xx#minimal.tmp.cram
  ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
  ./test_view -@4 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
  ./test_view -@4 xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
  ./test_view -@4 xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
.. ok

test_view testing xx#pair.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#pair.sam > xx#pair.tmp.bam
  ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
  ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam
  ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
  ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram
  ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
  ./test_view -@4 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
  ./test_view -@4 xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#pair.sam > xx#pair.tmp.cram
  ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
  ./test_view -@4 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
  ./test_view -@4 xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
  ./test_view -@4 xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
.. ok

test_view testing xx#repeated.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#repeated.sam > xx#repeated.tmp.bam
  ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
  ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam
  ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
  ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram
  ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
  ./test_view -@4 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
  ./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#repeated.sam > xx#repeated.tmp.cram
  ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
  ./test_view -@4 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
  ./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
  ./test_view -@4 xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
.. ok

test_view testing xx#rg.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#rg.sam > xx#rg.tmp.bam
  ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
  ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam
  ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
  ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram
  ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
  ./test_view -@4 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
  ./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#rg.sam > xx#rg.tmp.cram
  ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
  ./test_view -@4 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
  ./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
  ./test_view -@4 xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
.. ok

test_view testing xx#tlen.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#tlen.sam > xx#tlen.tmp.bam
  ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
  ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam
  ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
  ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram
  ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
  ./test_view -@4 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
  ./test_view -@4 xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen.sam > xx#tlen.tmp.cram
  ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
  ./test_view -@4 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
  ./test_view -@4 xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
  ./test_view -@4 xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
.. ok

test_view testing xx#tlen2.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#tlen2.sam > xx#tlen2.tmp.bam
  ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
  ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam
  ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
  ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram
  ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
  ./test_view -@4 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
  ./test_view -@4 xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen2.sam > xx#tlen2.tmp.cram
  ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
  ./test_view -@4 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
  ./test_view -@4 xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
  ./test_view -@4 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
.. ok

test_view testing xx#triplet.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#triplet.sam > xx#triplet.tmp.bam
  ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
  ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam
  ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
  ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram
  ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
  ./test_view -@4 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
  ./test_view -@4 xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#triplet.sam > xx#triplet.tmp.cram
  ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
  ./test_view -@4 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
  ./test_view -@4 xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
  ./test_view -@4 xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
.. ok

test_view testing xx#unsorted.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#unsorted.sam > xx#unsorted.tmp.bam
  ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
  ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam
  ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
  ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram
  ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
  ./test_view -@4 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
  ./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#unsorted.sam > xx#unsorted.tmp.cram
  ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
  ./test_view -@4 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
  ./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
  ./test_view -@4 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok

  ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
  ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
test_vcf_api:
	/<<PKGBUILDDIR>>/test/test-vcf-api /tmp/_CYf9bMBA1/test-vcf-api.bcf
.. ok

test_vcf_sweep:
	/<<PKGBUILDDIR>>/test/test-vcf-sweep /tmp/_CYf9bMBA1/test-vcf-api.bcf
.. ok

test_vcf_various:
	/<<PKGBUILDDIR>>/htsfile -ch /<<PKGBUILDDIR>>/test/test-vcf-hdr-in.vcf
.. ok

test_vcf_various:
	/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/formatcols.vcf
.. ok

test_vcf_various:
	/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/noroundtrip.vcf
.. ok

test_vcf_various:
	/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/formatmissing.vcf
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/_CYf9bMBA1 -s 1006172129
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/_CYf9bMBA1 -s 81672992
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/_CYf9bMBA1 -s 1224817017
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/_CYf9bMBA1 -s 832682054
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/_CYf9bMBA1 -s 147523214
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/_CYf9bMBA1 -s 612446139
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/_CYf9bMBA1 -s 815446864
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/_CYf9bMBA1 -s 824287649
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/_CYf9bMBA1 -s 1014346550
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/_CYf9bMBA1 -s 1081233135
.. ok

test_command:
	/<<PKGBUILDDIR>>/test/test-bcf-translate -
.. ok

test_convert_padded_header:
	/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/_CYf9bMBA1/headernul0.bam
.. ok

test_convert_padded_header:
	/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/_CYf9bMBA1/headernul1.bam
.. ok

test_convert_padded_header:
	/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/_CYf9bMBA1/headernul678.bam
.. ok

test_rebgzip: Alternate zlib/deflate library detected
test_rebgzip:
	/<<PKGBUILDDIR>>/bgzip -I /<<PKGBUILDDIR>>/test/bgziptest.txt.tmp.gz.gzi -c -g /<<PKGBUILDDIR>>/test/bgziptest.txt
.. ok

test-logging:
	/<<PKGBUILDDIR>>/test/test-logging.pl
.. ok

test_realn:
	/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok

test_realn:
	/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok

test_realn:
	/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok

test_realn:
	/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok

test_realn:
	/<<PKGBUILDDIR>>/test/test_realn -e -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok

test_realn:
	/<<PKGBUILDDIR>>/test/test_realn -e -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok

test_realn:
	/<<PKGBUILDDIR>>/test/test_realn -r -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02-r.sam -o -
.. ok

test_realn:
	/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02_exp.sam -o -
.. ok

test_realn:
	/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02_exp-a.sam -o -
.. ok


Number of tests:
    total   .. 97
    passed  .. 97
    failed  .. 0

make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
 fakeroot debian/rules binary-arch
dh binary-arch
   dh_testroot -a
   dh_prep -a
	rm -f -- debian/libhts2.substvars debian/libhts-dev.substvars debian/tabix.substvars
	rm -fr -- debian/.debhelper/generated/libhts2/ debian/libhts2/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/tabix/ debian/tabix/
	rm -f debian/libhts-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \
    rm /<<PKGBUILDDIR>>/test/${binary} ; \
done
dh_auto_install -- prefix=/usr
	install -d /<<PKGBUILDDIR>>/debian/tmp
	make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
make[2]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp/usr/bin /<<PKGBUILDDIR>>/debian/tmp/usr/include /<<PKGBUILDDIR>>/debian/tmp/usr/include/htslib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man5 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig
gcc -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c
if test -n ""; then mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp; fi
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.9#g' htslib.pc.tmp > /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
gcc -shared -Wl,-soname,libhts.so.2 -Wl,-z,relro -Wl,-z,now -Wl,-flto  -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
ln -sf libhts.so libhts.so.2
install -p -m 644 libhts.so /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.9
ln -sf libhts.so.1.9 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so
ln -sf libhts.so.1.9 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.2
install -p bgzip htsfile tabix /<<PKGBUILDDIR>>/debian/tmp/usr/bin
if test -n ""; then install -p  /<<PKGBUILDDIR>>/debian/tmp; fi
install -p -m 644 htslib/*.h /<<PKGBUILDDIR>>/debian/tmp/usr/include/htslib
install -p -m 644 libhts.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a
install -p -m 644 bgzip.1 htsfile.1 tabix.1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man5
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# restore clean copy of test dir before dh_install is run
# This should not be done earlier since dh_auto_install contains some unconditional removals
rm -f -r test
mv test_backup test
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install -a
	install -d debian/libhts2/usr/lib/arm-linux-gnueabihf
	cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.9 debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.2 debian/libhts2/usr/lib/arm-linux-gnueabihf/
	install -d debian/.debhelper/generated/libhts2
	install -d debian/libhts-dev/usr/include
	cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/
	install -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf
	cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so debian/libhts-dev/usr/lib/arm-linux-gnueabihf/
	install -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
	cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig/
	install -d debian/libhts-dev/usr/share/man/man5
	cp --reflink=auto -a debian/tmp/usr/share/man/man5/faidx.5 debian/tmp/usr/share/man/man5/sam.5 debian/tmp/usr/share/man/man5/vcf.5 debian/libhts-dev/usr/share/man/man5/
	install -d debian/.debhelper/generated/libhts-dev
	install -d debian/.debhelper/generated/libhts-private-dev
	install -d debian/.debhelper/generated/htslib-test
	install -d debian/tabix/usr/bin
	cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/
	install -d debian/.debhelper/generated/tabix
   dh_installdocs -a
	install -d debian/libhts2/usr/share/doc/libhts2
	install -p -m0644 debian/copyright debian/libhts2/usr/share/doc/libhts2/copyright
	install -d debian/libhts-dev/usr/share/doc/libhts-dev
	cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev
	chown -R 0:0 debian/libhts-dev/usr/share/doc
	chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc
	install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright
	install -d debian/tabix/usr/share/doc/tabix
	install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright
	rm -f debian/libhts-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log
   debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs NEWS
	install -p -m0644 debian/changelog debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian
	install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog
	install -p -m0644 debian/changelog debian/libhts2/usr/share/doc/libhts2/changelog.Debian
	install -p -m0644 NEWS debian/libhts2/usr/share/doc/libhts2/changelog
	install -p -m0644 debian/changelog debian/tabix/usr/share/doc/tabix/changelog.Debian
	install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installman -a
	install -d debian/tabix/usr/share/man/man1/
	install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1
	install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1
	man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/faidx.5 > debian/libhts-dev/usr/share/man/man5/faidx.5.dh-new
	man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/vcf.5 > debian/libhts-dev/usr/share/man/man5/vcf.5.dh-new
	man -l --recode UTF-8 ./debian/tabix/usr/share/man/man1/tabix.1 > debian/tabix/usr/share/man/man1/tabix.1.dh-new
	mv debian/libhts-dev/usr/share/man/man5/faidx.5.dh-new debian/libhts-dev/usr/share/man/man5/faidx.5
	man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/sam.5 > debian/libhts-dev/usr/share/man/man5/sam.5.dh-new
	mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1
	chmod 0644 -- debian/tabix/usr/share/man/man1/tabix.1
	mv debian/libhts-dev/usr/share/man/man5/vcf.5.dh-new debian/libhts-dev/usr/share/man/man5/vcf.5
	man -l --recode UTF-8 ./debian/tabix/usr/share/man/man1/htsfile.1 > debian/tabix/usr/share/man/man1/htsfile.1.dh-new
	mv debian/libhts-dev/usr/share/man/man5/sam.5.dh-new debian/libhts-dev/usr/share/man/man5/sam.5
	chmod 0644 -- debian/libhts-dev/usr/share/man/man5/faidx.5 debian/libhts-dev/usr/share/man/man5/sam.5
	mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1
	chmod 0644 -- debian/libhts-dev/usr/share/man/man5/vcf.5 debian/tabix/usr/share/man/man1/htsfile.1
   dh_perl -a
   dh_link -a
	rm -f debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.2
	ln -s libhts.so.1.9 debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.2
	rm -f debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
	ln -s libhts.so.1.9 debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
	rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz
	ln -s tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz
   dh_strip_nondeterminism -a
   dh_compress -a
	cd debian/libhts2
	cd debian/tabix
	cd debian/libhts-dev
	chmod a-x usr/share/doc/libhts2/changelog usr/share/doc/libhts2/changelog.Debian
	chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
	gzip -9nf usr/share/doc/libhts2/changelog usr/share/doc/libhts2/changelog.Debian
	chmod a-x usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5
	gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
	cd '/<<PKGBUILDDIR>>'
	gzip -9nf usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5
	cd '/<<PKGBUILDDIR>>'
	cd '/<<PKGBUILDDIR>>'
   dh_fixperms -a
	find debian/libhts2 -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
	find debian/tabix -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
	find debian/libhts-dev -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
	find debian/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/libhts2 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/libhts2/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts2/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhts2/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/libhts2 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhts-dev/usr/share/man debian/libhts-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhts2/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
	find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
	find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
   dh_missing -a
   dh_strip -a
	install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/87
	objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/87/39b42a500f502e0f5f49b1d289868924a93f68.debug
	install -d debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/1a
	objcopy --only-keep-debug --compress-debug-sections debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9 debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/1a/e996904377cba9c9608eaba19c84e90e9b03da.debug
	strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.a
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/87/39b42a500f502e0f5f49b1d289868924a93f68.debug
	chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/87/39b42a500f502e0f5f49b1d289868924a93f68.debug
	strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip
	objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/87/39b42a500f502e0f5f49b1d289868924a93f68.debug debian/tabix/usr/bin/bgzip
	install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e7
	objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e7/08b35f459f86a266d00902402050789fca3cdc.debug
	chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/1a/e996904377cba9c9608eaba19c84e90e9b03da.debug
	chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/1a/e996904377cba9c9608eaba19c84e90e9b03da.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9
	objcopy --add-gnu-debuglink debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/1a/e996904377cba9c9608eaba19c84e90e9b03da.debug debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/kfunc.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/knetfile.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/kstring.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/bcf_sr_sort.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/bgzf.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/errmod.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/faidx.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/hfile.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/hfile_net.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/hts.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/hts_os.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/md5.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/multipart.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/probaln.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/realn.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/regidx.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/sam.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/synced_bcf_reader.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/vcf_sweep.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/tbx.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/textutils.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/thread_pool.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/vcf.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/vcfutils.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/cram_codecs.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/cram_decode.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/cram_encode.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/cram_external.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/cram_index.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/cram_io.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/cram_samtools.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/cram_stats.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/files.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/mFILE.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/open_trace_file.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/pooled_alloc.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/rANS_static.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/sam_header.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/string_alloc.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/hfile_libcurl.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/hfile_gcs.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stkMB1kx/hfile_s3.o: plugin needed to handle lto object
	install -d debian/.debhelper/libhts2/dbgsym-root/usr/share/doc
	ln -s libhts2 debian/.debhelper/libhts2/dbgsym-root/usr/share/doc/libhts2-dbgsym
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e7/08b35f459f86a266d00902402050789fca3cdc.debug
	chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e7/08b35f459f86a266d00902402050789fca3cdc.debug
	strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/htsfile
	objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e7/08b35f459f86a266d00902402050789fca3cdc.debug debian/tabix/usr/bin/htsfile
	install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/22
	objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/22/21cac69b8255b36d8cc8f8c5135ca1ec8233cb.debug
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/22/21cac69b8255b36d8cc8f8c5135ca1ec8233cb.debug
	chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/22/21cac69b8255b36d8cc8f8c5135ca1ec8233cb.debug
	strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix
	objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/22/21cac69b8255b36d8cc8f8c5135ca1ec8233cb.debug debian/tabix/usr/bin/tabix
	install -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc
	ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym
   dh_makeshlibs -a
	rm -f debian/libhts2/DEBIAN/shlibs
	install -d debian/libhts2/DEBIAN
	echo "libhts 2 libhts2" >> debian/libhts2/DEBIAN/shlibs
	chmod 0644 -- debian/libhts2/DEBIAN/shlibs
	chown 0:0 -- debian/libhts2/DEBIAN/shlibs
	dpkg-gensymbols -plibhts2 -Idebian/libhts2.symbols -Pdebian/libhts2 -edebian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9
	mv debian/.debhelper/generated/libhts2/triggers.new debian/.debhelper/generated/libhts2/triggers
	rm -f debian/libhts-dev/DEBIAN/shlibs
	rm -f debian/tabix/DEBIAN/shlibs
   dh_shlibdeps -a
	dpkg-shlibdeps -Tdebian/libhts2.substvars debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9
	install -d debian/tabix/DEBIAN
	dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/tabix debian/tabix/usr/bin/htsfile were not linked against libm.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/tabix debian/tabix/usr/bin/htsfile were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
   dh_installdeb -a
	install -p -m0644 debian/.debhelper/generated/libhts2/triggers debian/libhts2/DEBIAN/triggers
	install -d debian/libhts-dev/DEBIAN
   dh_gencontrol -a
	echo misc:Depends= >> debian/libhts-dev.substvars
	echo misc:Pre-Depends= >> debian/libhts-dev.substvars
	dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -Pdebian/libhts-dev
	echo misc:Depends= >> debian/libhts2.substvars
	echo misc:Pre-Depends= >> debian/libhts2.substvars
	install -d debian/.debhelper/libhts2/dbgsym-root/DEBIAN
	dpkg-gencontrol -plibhts2 -ldebian/changelog -Tdebian/libhts2.substvars -Pdebian/.debhelper/libhts2/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=libhts2-dbgsym "-DDepends=libhts2 (= \${binary:Version})" "-DDescription=debug symbols for libhts2" -DBuild-Ids=1ae996904377cba9c9608eaba19c84e90e9b03da -DSection=debug -UReplaces -UBreaks
	echo misc:Depends= >> debian/tabix.substvars
	echo misc:Pre-Depends= >> debian/tabix.substvars
	install -d debian/.debhelper/tabix/dbgsym-root/DEBIAN
	dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=2221cac69b8255b36d8cc8f8c5135ca1ec8233cb 8739b42a500f502e0f5f49b1d289868924a93f68 e708b35f459f86a266d00902402050789fca3cdc" -DSection=debug -UReplaces -UBreaks
	chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/control
	chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -plibhts2 -ldebian/changelog -Tdebian/libhts2.substvars -Pdebian/libhts2
	chmod 0644 -- debian/libhts-dev/DEBIAN/control
	chown 0:0 -- debian/libhts-dev/DEBIAN/control
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control
	chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix
	chmod 0644 -- debian/libhts2/DEBIAN/control
	chown 0:0 -- debian/libhts2/DEBIAN/control
	chmod 0644 -- debian/tabix/DEBIAN/control
	chown 0:0 -- debian/tabix/DEBIAN/control
   dh_md5sums -a
	cd debian/libhts2 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/libhts2/DEBIAN/md5sums
	chown 0:0 -- debian/libhts2/DEBIAN/md5sums
	chmod 0644 -- debian/tabix/DEBIAN/md5sums
	chown 0:0 -- debian/tabix/DEBIAN/md5sums
	cd debian/.debhelper/libhts2/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums
	chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/md5sums
	chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/md5sums
	chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums
	chown 0:0 -- debian/libhts-dev/DEBIAN/md5sums
   dh_builddeb -a
	dpkg-deb --build debian/libhts2 ..
	dpkg-deb --build debian/libhts-dev ..
	dpkg-deb --build debian/.debhelper/tabix/dbgsym-root ..
dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.9-10_armhf.deb'.
dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.9-10_armhf.deb'.
dpkg-deb: building package 'libhts2' in '../libhts2_1.9-10_armhf.deb'.
	dpkg-deb --build debian/.debhelper/libhts2/dbgsym-root ..
dpkg-deb: building package 'libhts2-dbgsym' in '../libhts2-dbgsym_1.9-10_armhf.deb'.
	dpkg-deb --build debian/tabix ..
dpkg-deb: building package 'tabix' in '../tabix_1.9-10_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../htslib_1.9-10_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-source: info: using options from htslib-1.9/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-03-02T17:15:43Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


htslib_1.9-10_armhf.changes:
----------------------------

Format: 1.8
Date: Wed, 16 Jan 2019 05:23:22 -0800
Source: htslib
Binary: libhts2 libhts-dev libhts-private-dev htslib-test tabix
Architecture: armhf
Version: 1.9-10
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <michael.crusoe@gmail.com>
Description:
 htslib-test - Test data for HTSlib
 libhts-dev - development files for the HTSlib
 libhts-private-dev - private development files for the HTSlib (use with care)
 libhts2    - C library for high-throughput sequencing data formats
 tabix      - generic indexer for TAB-delimited genome position files
Changes:
 htslib (1.9-10) unstable; urgency=medium
 .
   * Bring the libdeflate, GCS, and S3 updates back to unstable.
Checksums-Sha1:
 747519125b1e5654272e80f4fa6208017d78b929 6079 htslib_1.9-10_armhf.buildinfo
 2d6db2dcdfa5da1bede34270cd9d8c16ab8ce5b4 4284164 libhts-dev_1.9-10_armhf.deb
 99eb9cfb723a3833139b732c509597ed95cb5d52 217672 libhts2-dbgsym_1.9-10_armhf.deb
 365cedfcae81406e9ce076a2be200fd079da0d46 254372 libhts2_1.9-10_armhf.deb
 1f17313079635a5ff058a0a08c6c75088858cba1 512596 tabix-dbgsym_1.9-10_armhf.deb
 ef73106629a00f53cd53ceca95bb9aca530e5e9f 239300 tabix_1.9-10_armhf.deb
Checksums-Sha256:
 18070d046aba496127e3207cb566385b2c5cdd2e878ec6b0cadb7e0c779000b5 6079 htslib_1.9-10_armhf.buildinfo
 68b1c7f6a6d383ef76066fd133e08401f14c08fea9a89c3087fba6be745120e2 4284164 libhts-dev_1.9-10_armhf.deb
 2928405ed45092dc10fc488edb6daa82a97c387147c8574c88a4bfef74413c30 217672 libhts2-dbgsym_1.9-10_armhf.deb
 2718432a6abf9c396e3fb1b28cbfe90f9d1999e6694f45556301f84d8e58b439 254372 libhts2_1.9-10_armhf.deb
 f64b6bd8d493fb4c25660e0a580feeb634e97025560ad898e2176701113ef3a2 512596 tabix-dbgsym_1.9-10_armhf.deb
 9438f39d65fd2e4259e1e8aeb0891ff9f5db81f4532b1c932e2f4f08ed1fe2a9 239300 tabix_1.9-10_armhf.deb
Files:
 b655d583236d3f5f235e28c256632a97 6079 science optional htslib_1.9-10_armhf.buildinfo
 a19926f3fb0c7d50feee1be0eda791a3 4284164 libdevel optional libhts-dev_1.9-10_armhf.deb
 48d783632c878328910d04701ec1a9d9 217672 debug optional libhts2-dbgsym_1.9-10_armhf.deb
 e50ce5c4efc91101945ce016b32c4913 254372 libs optional libhts2_1.9-10_armhf.deb
 507e80bd03639ae7cbad4f334b152eb0 512596 debug optional tabix-dbgsym_1.9-10_armhf.deb
 d51c5771ec7f2d7ac9cf93b10ec43957 239300 science optional tabix_1.9-10_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


libhts-dev_1.9-10_armhf.deb
---------------------------

 new Debian package, version 2.0.
 size 4284164 bytes: control archive=1868 bytes.
    1046 bytes,    24 lines      control              
    2259 bytes,    35 lines      md5sums              
 Package: libhts-dev
 Source: htslib
 Version: 1.9-10
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5132
 Depends: libhts2 (= 1.9-10), liblzma-dev, zlib1g-dev
 Section: libdevel
 Priority: optional
 Multi-Arch: same
 Homepage: https://github.com/samtools/htslib
 Description: development files for the HTSlib
  HTSlib is an implementation of a unified C library for accessing common file
  formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
  Format), used for high-throughput sequencing data, and is the core library
  used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
  compatible with gcc, g++ and clang.
  .
  HTSlib implements a generalized BAM (binary SAM) index, with file extension
  ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
  new index and then for the old if the new index is absent.
  .
  This package contains development files for the HTSlib: headers, static
  library, manual pages, etc.

drwxr-xr-x root/root         0 2019-01-16 13:23 ./
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/include/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/include/htslib/
-rw-r--r-- root/root     14797 2018-07-18 08:33 ./usr/include/htslib/bgzf.h
-rw-r--r-- root/root     15393 2018-07-18 08:33 ./usr/include/htslib/cram.h
-rw-r--r-- root/root      8972 2018-07-18 08:33 ./usr/include/htslib/faidx.h
-rw-r--r-- root/root     10077 2018-07-18 08:33 ./usr/include/htslib/hfile.h
-rw-r--r-- root/root     30459 2018-07-18 08:33 ./usr/include/htslib/hts.h
-rw-r--r-- root/root      3336 2018-07-18 08:33 ./usr/include/htslib/hts_defs.h
-rw-r--r-- root/root     11446 2018-07-18 08:33 ./usr/include/htslib/hts_endian.h
-rw-r--r-- root/root      3898 2018-07-18 08:33 ./usr/include/htslib/hts_log.h
-rw-r--r-- root/root      1996 2018-07-18 08:33 ./usr/include/htslib/hts_os.h
-rw-r--r-- root/root      4195 2018-07-18 08:33 ./usr/include/htslib/kbitset.h
-rw-r--r-- root/root      2716 2018-07-18 08:33 ./usr/include/htslib/kfunc.h
-rw-r--r-- root/root     21540 2018-07-18 08:33 ./usr/include/htslib/khash.h
-rw-r--r-- root/root      3990 2018-07-18 08:33 ./usr/include/htslib/khash_str2int.h
-rw-r--r-- root/root      5086 2018-07-18 08:33 ./usr/include/htslib/klist.h
-rw-r--r-- root/root      2850 2018-07-18 08:33 ./usr/include/htslib/knetfile.h
-rw-r--r-- root/root      9139 2018-07-18 08:33 ./usr/include/htslib/kseq.h
-rw-r--r-- root/root     10567 2018-07-18 08:33 ./usr/include/htslib/ksort.h
-rw-r--r-- root/root      7012 2018-07-18 08:33 ./usr/include/htslib/kstring.h
-rw-r--r-- root/root      5834 2018-07-18 08:33 ./usr/include/htslib/regidx.h
-rw-r--r-- root/root     29580 2018-07-18 08:33 ./usr/include/htslib/sam.h
-rw-r--r-- root/root     14954 2018-07-18 08:33 ./usr/include/htslib/synced_bcf_reader.h
-rw-r--r-- root/root      3118 2018-07-18 08:33 ./usr/include/htslib/tbx.h
-rw-r--r-- root/root      9386 2018-07-18 08:33 ./usr/include/htslib/thread_pool.h
-rw-r--r-- root/root     43671 2018-07-18 08:33 ./usr/include/htslib/vcf.h
-rw-r--r-- root/root      1602 2018-07-18 08:33 ./usr/include/htslib/vcf_sweep.h
-rw-r--r-- root/root      4819 2018-07-18 08:33 ./usr/include/htslib/vcfutils.h
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root   4919324 2019-01-16 13:23 ./usr/lib/arm-linux-gnueabihf/libhts.a
lrwxrwxrwx root/root         0 2019-01-16 13:23 ./usr/lib/arm-linux-gnueabihf/libhts.so -> libhts.so.1.9
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root       583 2019-01-16 13:23 ./usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/doc/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/doc/libhts-dev/
-rw-r--r-- root/root       401 2018-12-11 01:59 ./usr/share/doc/libhts-dev/README.test
-rw-r--r-- root/root      4288 2019-01-16 13:23 ./usr/share/doc/libhts-dev/changelog.Debian.gz
-rw-r--r-- root/root      8097 2018-07-18 08:33 ./usr/share/doc/libhts-dev/changelog.gz
-rw-r--r-- root/root      5762 2018-12-11 02:07 ./usr/share/doc/libhts-dev/copyright
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/man/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/man/man5/
-rw-r--r-- root/root      2452 2019-01-16 13:23 ./usr/share/man/man5/faidx.5.gz
-rw-r--r-- root/root      1535 2019-01-16 13:23 ./usr/share/man/man5/sam.5.gz
-rw-r--r-- root/root      1854 2019-01-16 13:23 ./usr/share/man/man5/vcf.5.gz


libhts2-dbgsym_1.9-10_armhf.deb
-------------------------------

 new Debian package, version 2.0.
 size 217672 bytes: control archive=548 bytes.
     384 bytes,    13 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: libhts2-dbgsym
 Source: htslib
 Version: 1.9-10
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 309
 Depends: libhts2 (= 1.9-10)
 Section: debug
 Priority: optional
 Multi-Arch: same
 Description: debug symbols for libhts2
 Build-Ids: 1ae996904377cba9c9608eaba19c84e90e9b03da

drwxr-xr-x root/root         0 2019-01-16 13:23 ./
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/debug/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/debug/.build-id/1a/
-rw-r--r-- root/root    305424 2019-01-16 13:23 ./usr/lib/debug/.build-id/1a/e996904377cba9c9608eaba19c84e90e9b03da.debug
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/doc/
lrwxrwxrwx root/root         0 2019-01-16 13:23 ./usr/share/doc/libhts2-dbgsym -> libhts2


libhts2_1.9-10_armhf.deb
------------------------

 new Debian package, version 2.0.
 size 254372 bytes: control archive=4796 bytes.
    1125 bytes,    22 lines      control              
     287 bytes,     4 lines      md5sums              
      17 bytes,     1 lines      shlibs               
   20119 bytes,   747 lines      symbols              
      65 bytes,     2 lines      triggers             
 Package: libhts2
 Source: htslib
 Version: 1.9-10
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 624
 Depends: libbz2-1.0, libc6 (>= 2.23), libcurl3-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0)
 Breaks: python-pysam (<< 0.15~), python3-pysam (<< 0.15~)
 Section: libs
 Priority: optional
 Multi-Arch: same
 Homepage: https://github.com/samtools/htslib
 Description: C library for high-throughput sequencing data formats
  HTSlib is an implementation of a unified C library for accessing common file
  formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
  Format), used for high-throughput sequencing data, and is the core library
  used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
  compatible with gcc, g++ and clang.
  .
  HTSlib implements a generalized BAM (binary SAM) index, with file extension
  ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
  new index and then for the old if the new index is absent.

drwxr-xr-x root/root         0 2019-01-16 13:23 ./
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root    587180 2019-01-16 13:23 ./usr/lib/arm-linux-gnueabihf/libhts.so.1.9
lrwxrwxrwx root/root         0 2019-01-16 13:23 ./usr/lib/arm-linux-gnueabihf/libhts.so.2 -> libhts.so.1.9
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/doc/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/doc/libhts2/
-rw-r--r-- root/root      4288 2019-01-16 13:23 ./usr/share/doc/libhts2/changelog.Debian.gz
-rw-r--r-- root/root      8097 2018-07-18 08:33 ./usr/share/doc/libhts2/changelog.gz
-rw-r--r-- root/root      5762 2018-12-11 02:07 ./usr/share/doc/libhts2/copyright


tabix-dbgsym_1.9-10_armhf.deb
-----------------------------

 new Debian package, version 2.0.
 size 512596 bytes: control archive=660 bytes.
     443 bytes,    12 lines      control              
     318 bytes,     3 lines      md5sums              
 Package: tabix-dbgsym
 Source: htslib
 Version: 1.9-10
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 682
 Depends: tabix (= 1.9-10)
 Section: debug
 Priority: optional
 Description: debug symbols for tabix
 Build-Ids: 2221cac69b8255b36d8cc8f8c5135ca1ec8233cb 8739b42a500f502e0f5f49b1d289868924a93f68 e708b35f459f86a266d00902402050789fca3cdc

drwxr-xr-x root/root         0 2019-01-16 13:23 ./
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/debug/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/debug/.build-id/22/
-rw-r--r-- root/root    245636 2019-01-16 13:23 ./usr/lib/debug/.build-id/22/21cac69b8255b36d8cc8f8c5135ca1ec8233cb.debug
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/debug/.build-id/87/
-rw-r--r-- root/root    197764 2019-01-16 13:23 ./usr/lib/debug/.build-id/87/39b42a500f502e0f5f49b1d289868924a93f68.debug
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/lib/debug/.build-id/e7/
-rw-r--r-- root/root    240744 2019-01-16 13:23 ./usr/lib/debug/.build-id/e7/08b35f459f86a266d00902402050789fca3cdc.debug
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/doc/
lrwxrwxrwx root/root         0 2019-01-16 13:23 ./usr/share/doc/tabix-dbgsym -> tabix


tabix_1.9-10_armhf.deb
----------------------

 new Debian package, version 2.0.
 size 239300 bytes: control archive=1108 bytes.
     964 bytes,    19 lines      control              
     481 bytes,     8 lines      md5sums              
 Package: tabix
 Source: htslib
 Version: 1.9-10
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 804
 Depends: libbz2-1.0, libc6 (>= 2.15), libcurl3-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0)
 Section: science
 Priority: optional
 Homepage: https://github.com/samtools/htslib
 Description: generic indexer for TAB-delimited genome position files
  Tabix indexes files where some columns indicate sequence coordinates: name
  (usually a chromosome), start and stop. The input data file must be position
  sorted and compressed by bgzip (provided in this package), which has a gzip
  like interface. After indexing, tabix is able to quickly retrieve data lines by
  chromosomal coordinates. Fast data retrieval also works over network if an URI
  is given as a file name.
  .
  This version of tabix is built from the HTSlib source.

drwxr-xr-x root/root         0 2019-01-16 13:23 ./
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/bin/
-rwxr-xr-x root/root     83412 2019-01-16 13:23 ./usr/bin/bgzip
-rwxr-xr-x root/root    353756 2019-01-16 13:23 ./usr/bin/htsfile
-rwxr-xr-x root/root    349652 2019-01-16 13:23 ./usr/bin/tabix
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/doc/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/doc/tabix/
-rw-r--r-- root/root      4288 2019-01-16 13:23 ./usr/share/doc/tabix/changelog.Debian.gz
-rw-r--r-- root/root      8097 2018-07-18 08:33 ./usr/share/doc/tabix/changelog.gz
-rw-r--r-- root/root      5762 2018-12-11 02:07 ./usr/share/doc/tabix/copyright
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/man/
drwxr-xr-x root/root         0 2019-01-16 13:23 ./usr/share/man/man1/
lrwxrwxrwx root/root         0 2019-01-16 13:23 ./usr/share/man/man1/bgzip.1.gz -> tabix.1.gz
-rw-r--r-- root/root      1700 2019-01-16 13:23 ./usr/share/man/man1/htsfile.1.gz
-rw-r--r-- root/root      2770 2019-01-16 13:23 ./usr/share/man/man1/tabix.1.gz


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| Post Build                                                                   |
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| Cleanup                                                                      |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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| Summary                                                                      |
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Build Architecture: armhf
Build-Space: 47496
Build-Time: 1581
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 310
Job: htslib_1.9-10
Machine Architecture: armhf
Package: htslib
Package-Time: 1944
Source-Version: 1.9-10
Space: 47496
Status: successful
Version: 1.9-10
--------------------------------------------------------------------------------
Finished at 2019-03-02T17:15:43Z
Build needed 00:32:24, 47496k disk space