Raspbian Package Auto-Building

Build log for htslib (1.5-2) on armhf

htslib1.5-2armhf → 2017-11-08 21:43:16

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01

+==============================================================================+
| htslib 1.5-2 (armhf)                         Wed, 08 Nov 2017 21:25:52 +0000 |
+==============================================================================+

Package: htslib
Version: 1.5-2
Source Version: 1.5-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/buster-staging-armhf-sbuild-bf3a49c3-bfc6-4ac0-b01b-1610feade445' 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 [10.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.2 MB]
Fetched 22.5 MB in 24s (900 kB/s)
Reading package lists...

+------------------------------------------------------------------------------+
| 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://anonscm.debian.org/git/debian-med/htslib.git -b debian/unstable
Please use:
git clone https://anonscm.debian.org/git/debian-med/htslib.git -b debian/unstable
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1157 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main htslib 1.5-2 (dsc) [2272 B]
Get:2 http://172.17.0.1/private buster-staging/main htslib 1.5-2 (tar) [1145 kB]
Get:3 http://172.17.0.1/private buster-staging/main htslib 1.5-2 (diff) [10.2 kB]
Fetched 1157 kB in 0s (4521 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/htslib-eTft5x/htslib-1.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/htslib-eTft5x' 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-x87OMs/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-x87OMs/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-x87OMs/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-x87OMs/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (3230 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-x87OMs/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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 e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
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 5 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15098 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) ...

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

Arch check ok (armhf included in any all)

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


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

Merged Build-Depends: debhelper (>= 10), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev
Filtered Build-Depends: debhelper (>= 10), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-htslib-dummy' in '/<<BUILDDIR>>/resolver-x87OMs/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-x87OMs/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Sources [529 B]
Get:5 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Packages [610 B]
Fetched 2472 B in 0s (3595 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-x87OMs/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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 e2fsprogs-l10n libsasl2-modules openssl
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 file gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
  libcurl3-gnutls libcurl4-gnutls-dev libfile-stripnondeterminism-perl
  libglib2.0-0 libgssapi-krb5-2 libicu57 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
  libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1
  libtimedate-perl libtool libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
  libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
  librtmp-dev libssh2-1-dev pkg-config krb5-doc krb5-user liblzma-doc
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser
  libmail-box-perl
Recommended packages:
  curl | wget | lynx-cur bzip2-doc libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs krb5-locales publicsuffix libssl-doc
  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 file gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
  libcurl3-gnutls libcurl4-gnutls-dev libfile-stripnondeterminism-perl
  libglib2.0-0 libgssapi-krb5-2 libicu57 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
  libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev
  libtimedate-perl libtool libxml2 m4 man-db po-debconf
  sbuild-build-depends-htslib-dummy zlib1g-dev
The following packages will be upgraded:
  libssl1.1
1 upgraded, 46 newly installed, 0 to remove and 4 not upgraded.
Need to get 23.1 MB of archives.
After this operation, 73.5 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-x87OMs/apt_archive ./ sbuild-build-depends-htslib-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-2 [95.8 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.14 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libssl1.1 armhf 1.1.0g-2 [1100 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-5 [609 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1+nmu1 [74.2 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.1-1 [2653 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.10.5 [978 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15.2-2 [58.6 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.15.2-2 [116 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15.2-2 [263 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.15.2-2 [133 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.27.0-1 [71.0 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.18.0-4 [42.4 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.56.1-1 [274 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libcurl4-gnutls-dev armhf 7.56.1-1 [342 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.2-1.3 [284 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.0g-2 [1371 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23 [24.9 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../39-libssh2-1_1.8.0-1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../40-libcurl3-gnutls_7.56.1-1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.56.1-1) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
Preparing to unpack .../41-libcurl4-gnutls-dev_7.56.1-1_armhf.deb ...
Unpacking libcurl4-gnutls-dev:armhf (7.56.1-1) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../42-liblzma-dev_5.2.2-1.3_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.2-1.3) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../43-libssl-dev_1.1.0g-2_armhf.deb ...
Unpacking libssl-dev:armhf (1.1.0g-2) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../44-zlib1g-dev_1%3a1.2.8.dfsg-5_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Selecting previously unselected package dh-exec.
Preparing to unpack .../45-dh-exec_0.23_armhf.deb ...
Unpacking dh-exec (0.23) ...
Selecting previously unselected package sbuild-build-depends-htslib-dummy.
Preparing to unpack .../46-sbuild-build-depends-htslib-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Setting up libbz2-dev:armhf (1.0.6-8.1) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libnghttp2-14:armhf (1.27.0-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.11-1) ...
Setting up libpsl5:armhf (0.18.0-4) ...
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.54.1-1) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.4.2-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-8) ...
Setting up libbsd0:armhf (0.8.6-2) ...
Setting up libxml2:armhf (2.9.4+dfsg1-5) ...
Setting up libmagic-mgc (1:5.32-1) ...
Setting up libmagic1:armhf (1:5.32-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.24-17) ...
Setting up autotools-dev (20161112.1+nmu1) ...
Setting up libssl1.1:armhf (1.1.0g-2) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.14) ...
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 autopoint (0.19.8.1-4) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up gettext (0.19.8.1-4) ...
Setting up libssl-dev:armhf (1.1.0g-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-1) ...
Setting up libkrb5support0:armhf (1.15.2-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.15.2-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libkrb5-3:armhf (1.15.2-2) ...
Setting up libgssapi-krb5-2:armhf (1.15.2-2) ...
Setting up libcurl3-gnutls:armhf (7.56.1-1) ...
Setting up libcurl4-gnutls-dev:armhf (7.56.1-1) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (10.10.5) ...
Setting up dh-autoreconf (14) ...
Setting up dh-exec (0.23) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-17) ...

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

Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.29.1-6+rpi1 dpkg-dev_1.19.0.4 g++-7_7.2.0-12 gcc-7_7.2.0-12 libc6-dev_2.24-17 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha3 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-6+rpi1 binutils-arm-linux-gnueabihf_2.29.1-6+rpi1 binutils-common_2.29.1-6+rpi1 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-12 dash_0.5.8-2.5 debconf_1.5.64 debhelper_10.10.5 debianutils_4.8.2 dh-autoreconf_14 dh-exec_0.23 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.1-5 dmsetup_2:1.02.142-1 dpkg_1.19.0.4 dpkg-dev_1.19.0.4 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 e2fsprogs-l10n_1.43.7-1 fakeroot_1.22-1 fdisk_2.30.2-0.1 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.2.0-1d1 g++-7_7.2.0-12 gcc_4:7.2.0-1d1 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_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-12 gcc-7-base_7.2.0-12 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.1-5 gnupg-agent_2.2.1-5 gnupg-l10n_2.2.1-5 gnupg-utils_2.2.1-5 gpg_2.2.1-5 gpg-agent_2.2.1-5 gpg-wks-client_2.2.1-5 gpg-wks-server_2.2.1-5 gpgconf_2.2.1-5 gpgsm_2.2.1-5 gpgv_2.2.1-5 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.1-2 libapt-pkg5.0_1.6~alpha3 libarchive-zip-perl_1.59-1 libasan4_7.2.0-12 libassuan0_2.4.3-3 libatomic1_7.2.0-12 libattr1_1:2.4.47-2 libaudit-common_1:2.8.1-1 libaudit1_1:2.8.1-1 libbinutils_2.29.1-6+rpi1 libblkid1_2.30.2-0.1 libbsd0_0.8.6-2 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.24-17 libc-dev-bin_2.24-17 libc6_2.24-17 libc6-dev_2.24-17 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.1 libcc1-0_7.2.0-12 libcilkrts5_7.2.0-12 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.56.1-1 libcurl4-gnutls-dev_7.56.1-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.22-1 libdebconfclient0_0.232 libdevmapper1.02.1_2:1.02.142-1 libdpkg-perl_1.19.0.4 libdrm-common_2.4.84-2+rpi1 libdrm2_2.4.84-2+rpi1 libfakeroot_1.22-1 libfdisk1_2.30.2-0.1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-12 libgcc1_1:7.2.0-12 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.16-1 libgomp1_7.2.0-12 libgpg-error0_1.27-4 libgssapi-krb5-2_1.15.2-2 libhogweed4_3.3-2 libicu57_57.1-8 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libk5crypto3_1.15.2-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libkrb5-3_1.15.2-2 libkrb5support0_1.15.2-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.1 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnghttp2-14_1.27.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.1-2 libpipeline1_1.4.2-1 libplymouth4_0.9.3-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libpsl5_0.18.0-4 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.30.2-0.1 libsqlite3-0_3.20.1-2 libss2_1.43.7-1 libssh2-1_1.8.0-1 libssl-dev_1.1.0g-2 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 libsystemd0_235-2 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-12 libudev1_235-2 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.1 libxml2_2.9.4+dfsg1-5 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.30.2-0.1 mountall_2.54 multiarch-support_2.24-17 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 openssl_1.1.0f-5 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-2 perl-base_5.26.1-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-2 pinentry-curses_1.0.0-3 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_235-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017c-1 udev_235-2 util-linux_2.30.2-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5

+------------------------------------------------------------------------------+
| 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 Nov  8 07:27:26 2017 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./htslib_1.5-2.dsc
dpkg-source: info: extracting htslib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking htslib_1.5.orig.tar.gz
dpkg-source: info: unpacking htslib_1.5-2.debian.tar.xz
dpkg-source: info: applying define_PATH_MAX.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying fix_pkg-config.patch
dpkg-source: info: applying htslib-add-cram_to_bam.patch
dpkg-source: info: applying fPIC.patch
dpkg-source: info: applying 877670.patch

Check disc space
----------------

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=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-bf3a49c3-bfc6-4ac0-b01b-1610feade445
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

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

dpkg-buildpackage: info: source package htslib
dpkg-buildpackage: info: source version 1.5-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build htslib-1.5
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from htslib-1.5/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$
 fakeroot debian/rules clean
dh clean
   dh_auto_clean
	make -j4 distclean
make[1]: 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-regidx test/test_view test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr 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[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_autoreconf_clean
   dh_clean
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/libhts2.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files
	rm -fr -- debian/libhts2/ debian/tmp/ debian/libhts-dev/ debian/htslib-test/ debian/tabix/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -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 {} + > debian/autoreconf.before
	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 {} + > debian/autoreconf.after
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
autoconf
./configure --enable-libcurl
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 special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking shared library type... plain .so
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
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 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 connect... 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 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
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   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)" \
# re-try later	  LDLIBS=-lhts \
  PACKAGE_VERSION="1.5-2" \
  libdir=/usr/lib/arm-linux-gnueabihf
	make -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-strict-aliasing" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.5"' > version.h
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -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 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 -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
ln -sf libhts.so libhts.so.2
gcc -Wl,-z,relro -Wl,-z,now -o test/hts_endian test/hts_endian.o -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 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 -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test
	make -j4 test VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
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/test-regidx
cd test && REF_PATH=: ./test.pl
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  -t auxf.fa -S -C 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 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 -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  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  -t c1.fa -S -C 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 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 -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  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  -t c1.fa -S -C 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 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 -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  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  -t c1.fa -S -C 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 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 -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  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  -t c1.fa -S -C 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 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 -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  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  -t c1.fa -S -C 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 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 -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  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  -t c1.fa -S -C 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 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 -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  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  -t c1.fa -S -C 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 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 -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  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  -t c2.fa -S -C 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 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 -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  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  -t ce.fa -S -C 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 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 -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  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#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  -t ce.fa -S -C 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 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 -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  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  -t ce.fa -S -C 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 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 -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  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  -t ce.fa -S -C 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 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 -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  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  -t ce.fa -S -C 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 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 -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  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  -t ce.fa -S -C 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 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 -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  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  -t ce.fa -S -C 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 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 -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  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  -t ce.fa -S -C 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 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 -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  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  -t ce.fa -S -C 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 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 -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  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  -t ce.fa -S -C 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 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 -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  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  -t ce.fa -S -C 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 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 -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  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  -t md.fa -S -C 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 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 -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  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  -t xx.fa -S -C 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 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 -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  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  -t xx.fa -S -C 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 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 -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  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_
WARNING: 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  -t xx.fa -S -C 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 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 -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  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  -t xx.fa -S -C 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 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 -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  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  -t xx.fa -S -C 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 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 -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  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  -t xx.fa -S -C 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 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 -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  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  -t xx.fa -S -C 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 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 -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  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  -t xx.fa -S -C 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 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 -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  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  -t xx.fa -S -C 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 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 -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  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  -t xx.fa -S -C 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 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 -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  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  -t xx.fa -S -C 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 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 -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  xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok

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 -t auxf.fa -S -C 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 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 -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 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 -t c1.fa -S -C 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 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 -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 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 -t c1.fa -S -C 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 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 -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 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 -t c1.fa -S -C 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 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 -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 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 -t c1.fa -S -C 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 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 -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 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 -t c1.fa -S -C 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 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 -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 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 -t c1.fa -S -C 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 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 -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 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 -t c1.fa -S -C 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 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 -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 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 -t c2.fa -S -C 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 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 -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 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 -t ce.fa -S -C 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 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 -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 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#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 -t ce.fa -S -C 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 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 -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 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 -t ce.fa -S -C 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 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 -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 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 -t ce.fa -S -C 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 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 -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 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 -t ce.fa -S -C 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 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 -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 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 -t ce.fa -S -C 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 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 -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 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 -t ce.fa -S -C 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 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 -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 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 -t ce.fa -S -C 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 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 -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 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 -t ce.fa -S -C 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 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 -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 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 -t ce.fa -S -C 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 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 -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 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 -t ce.fa -S -C 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 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 -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 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 -t md.fa -S -C 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 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 -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 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 -t xx.fa -S -C 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 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 -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 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 -t xx.fa -S -C 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 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 -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 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_
WARNING: 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 -t xx.fa -S -C 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 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 -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 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 -t xx.fa -S -C 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 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 -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 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 -t xx.fa -S -C 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 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 -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 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 -t xx.fa -S -C 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 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 -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 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 -t xx.fa -S -C 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 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 -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 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 -t xx.fa -S -C 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 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 -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 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 -t xx.fa -S -C 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 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 -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 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 -t xx.fa -S -C 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 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 -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 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 -t xx.fa -S -C 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 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 -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 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok

test_vcf_api:
	/<<PKGBUILDDIR>>/test/test-vcf-api /tmp/sifBofPKtz/test-vcf-api.bcf
.. ok

test_vcf_sweep:
	/<<PKGBUILDDIR>>/test/test-vcf-sweep /tmp/sifBofPKtz/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/sifBofPKtz -s 71759454
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/sifBofPKtz -s 575116714
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/sifBofPKtz -s 891210563
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/sifBofPKtz -s 91104695
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/sifBofPKtz -s 1174761024
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/sifBofPKtz -s 857418612
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/sifBofPKtz -s 477405764
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/sifBofPKtz -s 965784622
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/sifBofPKtz -s 930361955
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/sifBofPKtz -s 1289483957
.. ok

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

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

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

test_rebgzip:
	/<<PKGBUILDDIR>>/bgzip -I /<<PKGBUILDDIR>>/test/bgziptest.txt.gz.gzi -c -g /<<PKGBUILDDIR>>/test/bgziptest.txt
.. ok

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


Number of tests:
    total   .. 85
    passed  .. 85
    failed  .. 0

make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f test/*.tmp test/*.tmp.* test/*.o test/*.dSYM \
              test/fieldarith test/hfile test/test_view test/test-vcf-api test/test-vcf-sweep
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 \
  libdir=/usr/lib/arm-linux-gnueabihf \
  PACKAGE_VERSION="1.5-2"
	install -d debian/libhts2 debian/libhts-dev debian/tabix
	make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr libdir=/usr/lib/arm-linux-gnueabihf PACKAGE_VERSION=1.5-2
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
if test -n ""; then mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp; fi
install -p -m 644 libhts.so /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.5-2
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.5-2#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
ln -sf libhts.so.1.5-2 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so
ln -sf libhts.so.1.5-2 /<<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 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>>'
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.1.5-2 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/include/htslib/cram
	cp --reflink=auto -a ./cram/cram.h ./cram/cram_codecs.h ./cram/cram_decode.h ./cram/cram_encode.h ./cram/cram_index.h ./cram/cram_io.h ./cram/cram_samtools.h ./cram/cram_stats.h ./cram/cram_structs.h ./cram/mFILE.h ./cram/misc.h ./cram/open_trace_file.h ./cram/os.h ./cram/pooled_alloc.h ./cram/rANS_byte.h ./cram/rANS_static.h ./cram/sam_header.h ./cram/string_alloc.h debian/libhts-dev/usr/include/htslib/cram/
	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/lib/htslib
	cp --reflink=auto -a ./htslib.mk ./htslib_vars.mk debian/libhts-dev/usr/lib/htslib/
	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/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
	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/tabix/usr/share/doc/tabix/changelog.Debian
	install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/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
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/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/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/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
	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
   dh_lintian -a
	install -d debian/libhts2/usr/share/lintian/overrides
	install -p -m0644 debian/libhts2.lintian-overrides debian/libhts2/usr/share/lintian/overrides/libhts2
	install -d debian/tabix/usr/share/lintian/overrides
	install -p -m0644 debian/tabix.lintian-overrides debian/tabix/usr/share/lintian/overrides/tabix
   dh_perl -a
   dh_link -a
	rm -f debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.2
	ln -s libhts.so.1.5-2 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.1.5-2 debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
	rm -f debian/libhts-dev/usr/lib/htslib/htslib
	ln -s ../../include/htslib debian/libhts-dev/usr/lib/htslib/htslib
	rm -f debian/libhts-dev/usr/lib/htslib/bgzip
	ln -s ../../bin/bgzip debian/libhts-dev/usr/lib/htslib/bgzip
	rm -f debian/libhts-dev/usr/lib/htslib/tabix
	ln -s ../../bin/tabix debian/libhts-dev/usr/lib/htslib/tabix
	rm -f debian/libhts-dev/usr/lib/htslib/libhts.a
	ln -s ../arm-linux-gnueabihf/libhts.a debian/libhts-dev/usr/lib/htslib/libhts.a
	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
	Using 1510125866 as canonical time
	Normalizing debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.a using File::StripNondeterminism::handlers::ar
   dh_compress -a
	cd debian/libhts2
	cd debian/libhts-dev
	cd debian/tabix
	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
	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
	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
	chmod a-x usr/share/doc/libhts2/changelog usr/share/doc/libhts2/changelog.Debian
	gzip -9nf usr/share/doc/libhts2/changelog usr/share/doc/libhts2/changelog.Debian
	cd '/<<PKGBUILDDIR>>'
	cd '/<<PKGBUILDDIR>>'
	cd '/<<PKGBUILDDIR>>'
   dh_fixperms -a
	find debian/libhts2 -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/tabix -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
	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/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	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 f -a -true -a ! -regex 'debian/libhts2/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/tabix/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 f -a -true -a ! -regex 'debian/libhts-dev/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/tabix/usr/share/man debian/tabix/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/libhts2/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -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/libhts2 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
	find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -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/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
   dh_missing -a
   dh_strip -a
	strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.a
	install -d debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/5d
	objcopy --only-keep-debug --compress-debug-sections debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.5-2 debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/5d/b6387199eae378ba6021a5773b7efdd0a3ef2a.debug
	install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/5f
	objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/5f/921cd880baf7610b1ea66a1d2e7c4c80feecc4.debug
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/5f/921cd880baf7610b1ea66a1d2e7c4c80feecc4.debug
	chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/5f/921cd880baf7610b1ea66a1d2e7c4c80feecc4.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/5f/921cd880baf7610b1ea66a1d2e7c4c80feecc4.debug debian/tabix/usr/bin/bgzip
	install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d4
	objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d4/c70d96c21eb5632d83688e64904c5788bf495f.debug
	chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/5d/b6387199eae378ba6021a5773b7efdd0a3ef2a.debug
	chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/5d/b6387199eae378ba6021a5773b7efdd0a3ef2a.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.5-2
	objcopy --add-gnu-debuglink debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/5d/b6387199eae378ba6021a5773b7efdd0a3ef2a.debug debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.5-2
	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/d4/c70d96c21eb5632d83688e64904c5788bf495f.debug
	chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d4/c70d96c21eb5632d83688e64904c5788bf495f.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/d4/c70d96c21eb5632d83688e64904c5788bf495f.debug debian/tabix/usr/bin/htsfile
	install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8e
	objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8e/628c856227abe8f7a3a1f44f4b490c13e6b70a.debug
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8e/628c856227abe8f7a3a1f44f4b490c13e6b70a.debug
	chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8e/628c856227abe8f7a3a1f44f4b490c13e6b70a.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/8e/628c856227abe8f7a3a1f44f4b490c13e6b70a.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
	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.1.5-2
	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/tabix debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/bgzip were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tabix/usr/bin/tabix debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/bgzip were not linked against libm.so.6 (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=5db6387199eae378ba6021a5773b7efdd0a3ef2a -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=5f921cd880baf7610b1ea66a1d2e7c4c80feecc4 8e628c856227abe8f7a3a1f44f4b490c13e6b70a d4c70d96c21eb5632d83688e64904c5788bf495f" -DSection=debug -UReplaces -UBreaks
	chmod 0644 -- debian/libhts-dev/DEBIAN/control
	chown 0:0 -- debian/libhts-dev/DEBIAN/control
	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/.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/tabix/DEBIAN/control
	chown 0:0 -- debian/tabix/DEBIAN/control
	chmod 0644 -- debian/libhts2/DEBIAN/control
	chown 0:0 -- debian/libhts2/DEBIAN/control
   dh_md5sums -a
	(cd debian/libhts2 >/dev/null ; find . -type f  ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
	(cd debian/libhts-dev >/dev/null ; find . -type f  ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
	(cd debian/tabix >/dev/null ; find . -type f  ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
	chmod 0644 -- debian/libhts2/DEBIAN/md5sums
	chown 0:0 -- debian/libhts2/DEBIAN/md5sums
	(cd debian/.debhelper/libhts2/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
	chmod 0644 -- debian/tabix/DEBIAN/md5sums
	chown 0:0 -- debian/tabix/DEBIAN/md5sums
	(cd debian/.debhelper/tabix/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
	chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/md5sums
	chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums
	chown 0:0 -- debian/.debhelper/tabix/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 'libhts2' in '../libhts2_1.5-2_armhf.deb'.
dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.5-2_armhf.deb'.
dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.5-2_armhf.deb'.
	dpkg-deb --build debian/.debhelper/libhts2/dbgsym-root ..
dpkg-deb: building package 'libhts2-dbgsym' in '../libhts2-dbgsym_1.5-2_armhf.deb'.
	dpkg-deb --build debian/tabix ..
dpkg-deb: building package 'tabix' in '../tabix_1.5-2_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../htslib_1.5-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build htslib-1.5
dpkg-source: info: using options from htslib-1.5/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 2017-11-08T21:42:50Z

Finished
--------

I: Built successfully

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


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


htslib_1.5-2_armhf.changes:
---------------------------

Format: 1.8
Date: Wed, 08 Nov 2017 08:24:26 +0100
Source: htslib
Binary: libhts2 libhts-dev htslib-test tabix
Architecture: armhf
Version: 1.5-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 htslib-test - Test data for HTSlib
 libhts-dev - Development files for the HTSlib
 libhts2    - C library for high-throughput sequencing data formats
 tabix      - generic indexer for TAB-delimited genome position files
Closes: 877670
Changes:
 htslib (1.5-2) unstable; urgency=medium
 .
   * Apply patch provided by Graham Inggs <ginggs@debian.org> to fix FTBFS
     on armel armhf and ppc64el of bcftools
     Closes: #877670
   * Standards-Version: 4.1.1
Checksums-Sha1:
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 1d63b4aa38f14ce5c4b45dd516511f6c58a32777 336248 libhts-dev_1.5-2_armhf.deb
 d9077a19918f4aea28b69f86adf414f48d3d79c3 721392 libhts2-dbgsym_1.5-2_armhf.deb
 37035e4dca9d8a758f4cbc31debc9ac19146ad08 242492 libhts2_1.5-2_armhf.deb
 96b0af8a92f55e40a1d235768c4689ec52bb190d 1781800 tabix-dbgsym_1.5-2_armhf.deb
 15a3b80e33ebc360654c1f8a4066eb962770019c 246004 tabix_1.5-2_armhf.deb
Checksums-Sha256:
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 4d1bde2513bb2ac3fee962b23012d9d32f12c0e990ccc6002def7937178400e8 336248 libhts-dev_1.5-2_armhf.deb
 7cd3d26fc66b02c2a5081d993ac60cbe1e017c74c17f7b86de4e934a76d84c43 721392 libhts2-dbgsym_1.5-2_armhf.deb
 cfb5040c751f23c9d0b6f62b9f450916982788f3044360d4cca4c349000b665b 242492 libhts2_1.5-2_armhf.deb
 f19bd8379ee261e92556d6c806e37ee4481c5cf801d609754181506f7acaed09 1781800 tabix-dbgsym_1.5-2_armhf.deb
 d004ff12be4269cdf38e9b16d6cc05a3295dc3c44cc4346d7d5b3672a96bc5da 246004 tabix_1.5-2_armhf.deb
Files:
 cc938eaf5b6ca5ab3525f2932ceb13b0 5868 science optional htslib_1.5-2_armhf.buildinfo
 4cc36089de370f73fbc9c8ad16dd51a8 336248 libdevel optional libhts-dev_1.5-2_armhf.deb
 3981bc71188537206f95ab65402cd0a2 721392 debug optional libhts2-dbgsym_1.5-2_armhf.deb
 ad03fc9d0f3334bb87026e99381a47b4 242492 libs optional libhts2_1.5-2_armhf.deb
 23173136d55db64f9817308c3d97b2a8 1781800 debug optional tabix-dbgsym_1.5-2_armhf.deb
 fc3c594ac0ec88ede8df7a9982d39869 246004 science optional tabix_1.5-2_armhf.deb

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


libhts-dev_1.5-2_armhf.deb
--------------------------

 new Debian package, version 2.0.
 size 336248 bytes: control archive=2300 bytes.
    1039 bytes,    24 lines      control              
    3516 bytes,    53 lines      md5sums              
 Package: libhts-dev
 Source: htslib
 Version: 1.5-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1170
 Depends: libhts2 (= 1.5-2), liblzma-dev, tabix
 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 2017-11-08 07:24 ./
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/include/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/include/htslib/
-rw-r--r-- root/root     14541 2017-06-20 12:40 ./usr/include/htslib/bgzf.h
-rw-r--r-- root/root     15393 2017-06-20 12:40 ./usr/include/htslib/cram.h
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/include/htslib/cram/
-rw-r--r-- root/root      2419 2017-06-20 12:40 ./usr/include/htslib/cram/cram.h
-rw-r--r-- root/root      6174 2017-06-20 12:40 ./usr/include/htslib/cram/cram_codecs.h
-rw-r--r-- root/root      3633 2017-11-08 07:24 ./usr/include/htslib/cram/cram_decode.h
-rw-r--r-- root/root      3599 2017-06-20 12:40 ./usr/include/htslib/cram/cram_encode.h
-rw-r--r-- root/root      3363 2017-06-20 12:40 ./usr/include/htslib/cram/cram_index.h
-rw-r--r-- root/root     25085 2017-06-20 12:40 ./usr/include/htslib/cram/cram_io.h
-rw-r--r-- root/root      3583 2017-06-20 12:40 ./usr/include/htslib/cram/cram_samtools.h
-rw-r--r-- root/root      2279 2017-06-20 12:40 ./usr/include/htslib/cram/cram_stats.h
-rw-r--r-- root/root     23670 2017-06-20 12:40 ./usr/include/htslib/cram/cram_structs.h
-rw-r--r-- root/root      3020 2017-06-20 12:40 ./usr/include/htslib/cram/mFILE.h
-rw-r--r-- root/root      4306 2017-06-20 12:40 ./usr/include/htslib/cram/misc.h
-rw-r--r-- root/root      5025 2017-06-20 12:40 ./usr/include/htslib/cram/open_trace_file.h
-rw-r--r-- root/root      7526 2017-11-08 07:24 ./usr/include/htslib/cram/os.h
-rw-r--r-- root/root      2184 2017-06-20 12:40 ./usr/include/htslib/cram/pooled_alloc.h
-rw-r--r-- root/root     12255 2017-06-20 12:40 ./usr/include/htslib/cram/rANS_byte.h
-rw-r--r-- root/root      2033 2017-06-20 12:40 ./usr/include/htslib/cram/rANS_static.h
-rw-r--r-- root/root     14040 2017-06-20 12:40 ./usr/include/htslib/cram/sam_header.h
-rw-r--r-- root/root      2320 2017-06-20 12:40 ./usr/include/htslib/cram/string_alloc.h
-rw-r--r-- root/root      5696 2017-06-20 12:40 ./usr/include/htslib/faidx.h
-rw-r--r-- root/root      8754 2017-06-20 12:40 ./usr/include/htslib/hfile.h
-rw-r--r-- root/root     27544 2017-06-20 12:40 ./usr/include/htslib/hts.h
-rw-r--r-- root/root      2649 2017-06-20 12:40 ./usr/include/htslib/hts_defs.h
-rw-r--r-- root/root     11449 2017-06-20 12:40 ./usr/include/htslib/hts_endian.h
-rw-r--r-- root/root      3890 2017-06-20 12:40 ./usr/include/htslib/hts_log.h
-rw-r--r-- root/root      4195 2017-06-20 12:40 ./usr/include/htslib/kbitset.h
-rw-r--r-- root/root      2716 2017-06-20 12:40 ./usr/include/htslib/kfunc.h
-rw-r--r-- root/root     21540 2017-06-20 12:40 ./usr/include/htslib/khash.h
-rw-r--r-- root/root      3990 2017-06-20 12:40 ./usr/include/htslib/khash_str2int.h
-rw-r--r-- root/root      5086 2017-06-20 12:40 ./usr/include/htslib/klist.h
-rw-r--r-- root/root      2851 2017-06-20 12:40 ./usr/include/htslib/knetfile.h
-rw-r--r-- root/root      8900 2017-06-20 12:40 ./usr/include/htslib/kseq.h
-rw-r--r-- root/root     10152 2017-06-20 12:40 ./usr/include/htslib/ksort.h
-rw-r--r-- root/root      6933 2017-06-20 12:40 ./usr/include/htslib/kstring.h
-rw-r--r-- root/root      5845 2017-06-20 12:40 ./usr/include/htslib/regidx.h
-rw-r--r-- root/root     23677 2017-06-20 12:40 ./usr/include/htslib/sam.h
-rw-r--r-- root/root     14954 2017-06-20 12:40 ./usr/include/htslib/synced_bcf_reader.h
-rw-r--r-- root/root      3118 2017-06-20 12:40 ./usr/include/htslib/tbx.h
-rw-r--r-- root/root      9384 2017-06-20 12:40 ./usr/include/htslib/thread_pool.h
-rw-r--r-- root/root     43302 2017-06-20 12:40 ./usr/include/htslib/vcf.h
-rw-r--r-- root/root      1602 2017-06-20 12:40 ./usr/include/htslib/vcf_sweep.h
-rw-r--r-- root/root      4822 2017-06-20 12:40 ./usr/include/htslib/vcfutils.h
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root    733322 2017-11-08 07:24 ./usr/lib/arm-linux-gnueabihf/libhts.a
lrwxrwxrwx root/root         0 2017-11-08 07:24 ./usr/lib/arm-linux-gnueabihf/libhts.so -> libhts.so.1.5-2
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root       496 2017-11-08 07:24 ./usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/htslib/
lrwxrwxrwx root/root         0 2017-11-08 07:24 ./usr/lib/htslib/bgzip -> ../../bin/bgzip
lrwxrwxrwx root/root         0 2017-11-08 07:24 ./usr/lib/htslib/htslib -> ../../include/htslib
-rw-r--r-- root/root      5681 2017-06-20 12:40 ./usr/lib/htslib/htslib.mk
-rw-r--r-- root/root      2864 2017-06-20 12:40 ./usr/lib/htslib/htslib_vars.mk
lrwxrwxrwx root/root         0 2017-11-08 07:24 ./usr/lib/htslib/libhts.a -> ../arm-linux-gnueabihf/libhts.a
lrwxrwxrwx root/root         0 2017-11-08 07:24 ./usr/lib/htslib/tabix -> ../../bin/tabix
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/doc/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/doc/libhts-dev/
-rw-r--r-- root/root      2521 2017-11-08 07:24 ./usr/share/doc/libhts-dev/changelog.Debian.gz
-rw-r--r-- root/root      4840 2017-06-20 12:40 ./usr/share/doc/libhts-dev/changelog.gz
-rw-r--r-- root/root      5751 2017-11-08 07:24 ./usr/share/doc/libhts-dev/copyright
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/man/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/man/man5/
-rw-r--r-- root/root      2080 2017-11-08 07:24 ./usr/share/man/man5/faidx.5.gz
-rw-r--r-- root/root      1535 2017-11-08 07:24 ./usr/share/man/man5/sam.5.gz
-rw-r--r-- root/root      1854 2017-11-08 07:24 ./usr/share/man/man5/vcf.5.gz


libhts2-dbgsym_1.5-2_armhf.deb
------------------------------

 new Debian package, version 2.0.
 size 721392 bytes: control archive=548 bytes.
     382 bytes,    13 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: libhts2-dbgsym
 Source: htslib
 Version: 1.5-2
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 762
 Depends: libhts2 (= 1.5-2)
 Section: debug
 Priority: optional
 Multi-Arch: same
 Description: debug symbols for libhts2
 Build-Ids: 5db6387199eae378ba6021a5773b7efdd0a3ef2a

drwxr-xr-x root/root         0 2017-11-08 07:24 ./
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/debug/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/debug/.build-id/5d/
-rw-r--r-- root/root    769164 2017-11-08 07:24 ./usr/lib/debug/.build-id/5d/b6387199eae378ba6021a5773b7efdd0a3ef2a.debug
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/doc/
lrwxrwxrwx root/root         0 2017-11-08 07:24 ./usr/share/doc/libhts2-dbgsym -> libhts2


libhts2_1.5-2_armhf.deb
-----------------------

 new Debian package, version 2.0.
 size 242492 bytes: control archive=1168 bytes.
    1044 bytes,    21 lines      control              
     359 bytes,     5 lines      md5sums              
      17 bytes,     1 lines      shlibs               
      68 bytes,     2 lines      triggers             
 Package: libhts2
 Source: htslib
 Version: 1.5-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 614
 Depends: libbz2-1.0, libc6 (>= 2.23), libcurl3-gnutls (>= 7.18.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0)
 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 2017-11-08 07:24 ./
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root    599468 2017-11-08 07:24 ./usr/lib/arm-linux-gnueabihf/libhts.so.1.5-2
lrwxrwxrwx root/root         0 2017-11-08 07:24 ./usr/lib/arm-linux-gnueabihf/libhts.so.2 -> libhts.so.1.5-2
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/doc/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/doc/libhts2/
-rw-r--r-- root/root      2521 2017-11-08 07:24 ./usr/share/doc/libhts2/changelog.Debian.gz
-rw-r--r-- root/root      4840 2017-06-20 12:40 ./usr/share/doc/libhts2/changelog.gz
-rw-r--r-- root/root      5751 2017-11-08 07:24 ./usr/share/doc/libhts2/copyright
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/lintian/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/lintian/overrides/
-rw-r--r-- root/root       105 2017-11-08 07:24 ./usr/share/lintian/overrides/libhts2


tabix-dbgsym_1.5-2_armhf.deb
----------------------------

 new Debian package, version 2.0.
 size 1781800 bytes: control archive=652 bytes.
     442 bytes,    12 lines      control              
     318 bytes,     3 lines      md5sums              
 Package: tabix-dbgsym
 Source: htslib
 Version: 1.5-2
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1897
 Depends: tabix (= 1.5-2)
 Section: debug
 Priority: optional
 Description: debug symbols for tabix
 Build-Ids: 5f921cd880baf7610b1ea66a1d2e7c4c80feecc4 8e628c856227abe8f7a3a1f44f4b490c13e6b70a d4c70d96c21eb5632d83688e64904c5788bf495f

drwxr-xr-x root/root         0 2017-11-08 07:24 ./
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/debug/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/debug/.build-id/5f/
-rw-r--r-- root/root    573824 2017-11-08 07:24 ./usr/lib/debug/.build-id/5f/921cd880baf7610b1ea66a1d2e7c4c80feecc4.debug
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/debug/.build-id/8e/
-rw-r--r-- root/root    685448 2017-11-08 07:24 ./usr/lib/debug/.build-id/8e/628c856227abe8f7a3a1f44f4b490c13e6b70a.debug
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/lib/debug/.build-id/d4/
-rw-r--r-- root/root    669612 2017-11-08 07:24 ./usr/lib/debug/.build-id/d4/c70d96c21eb5632d83688e64904c5788bf495f.debug
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/doc/
lrwxrwxrwx root/root         0 2017-11-08 07:24 ./usr/share/doc/tabix-dbgsym -> tabix


tabix_1.5-2_armhf.deb
---------------------

 new Debian package, version 2.0.
 size 246004 bytes: control archive=1128 bytes.
     942 bytes,    19 lines      control              
     549 bytes,     9 lines      md5sums              
 Package: tabix
 Source: htslib
 Version: 1.5-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1358
 Depends: libbz2-1.0, libc6 (>= 2.15), libcurl3-gnutls (>= 7.18.0), 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 2017-11-08 07:24 ./
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/bin/
-rwxr-xr-x root/root    407000 2017-11-08 07:24 ./usr/bin/bgzip
-rwxr-xr-x root/root    468468 2017-11-08 07:24 ./usr/bin/htsfile
-rwxr-xr-x root/root    480752 2017-11-08 07:24 ./usr/bin/tabix
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/doc/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/doc/tabix/
-rw-r--r-- root/root      2521 2017-11-08 07:24 ./usr/share/doc/tabix/changelog.Debian.gz
-rw-r--r-- root/root      4840 2017-06-20 12:40 ./usr/share/doc/tabix/changelog.gz
-rw-r--r-- root/root      5751 2017-11-08 07:24 ./usr/share/doc/tabix/copyright
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/lintian/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/lintian/overrides/
-rw-r--r-- root/root       129 2017-11-08 07:24 ./usr/share/lintian/overrides/tabix
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/man/
drwxr-xr-x root/root         0 2017-11-08 07:24 ./usr/share/man/man1/
lrwxrwxrwx root/root         0 2017-11-08 07:24 ./usr/share/man/man1/bgzip.1.gz -> tabix.1.gz
-rw-r--r-- root/root      1697 2017-11-08 07:24 ./usr/share/man/man1/htsfile.1.gz
-rw-r--r-- root/root      2817 2017-11-08 07:24 ./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: 45356
Build-Time: 636
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 331
Job: htslib_1.5-2
Machine Architecture: armhf
Package: htslib
Package-Time: 1018
Source-Version: 1.5-2
Space: 45356
Status: successful
Version: 1.5-2
--------------------------------------------------------------------------------
Finished at 2017-11-08T21:42:50Z
Build needed 00:16:58, 45356k disc space