Raspbian Package Auto-Building

Build log for htslib (1.10.2-5) on armhf

htslib1.10.2-5armhf → 2020-08-05 05:31:04

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04

+==============================================================================+
| htslib 1.10.2-5 (armhf)                      Wed, 05 Aug 2020 04:56:31 +0000 |
+==============================================================================+

Package: htslib
Version: 1.10.2-5
Source Version: 1.10.2-5
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-8aee64db-bd41-4514-bed2-f7c3c9d40917' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.7 MB in 25s (1007 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'htslib' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/htslib.git
Please use:
git clone https://salsa.debian.org/med-team/htslib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1326 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main htslib 1.10.2-5 (dsc) [2368 B]
Get:2 http://172.17.0.1/private bullseye-staging/main htslib 1.10.2-5 (tar) [1306 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main htslib 1.10.2-5 (diff) [17.7 kB]
Fetched 1326 kB in 0s (7418 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/htslib-DLzjjY/htslib-1.10.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/htslib-DLzjjY' 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-ZwYIUu/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-ZwYIUu/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-ZwYIUu/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-ZwYIUu/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ZwYIUu/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ZwYIUu/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ZwYIUu/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ZwYIUu/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (2665 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  bsdextrautils libpam-cap netbase sensible-utils
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 19 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ZwYIUu/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.2 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12522 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Arch check ok (armhf included in any all)

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


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

Merged Build-Depends: debhelper-compat (= 13), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev
Filtered Build-Depends: debhelper-compat (= 13), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev
dpkg-deb: building package 'sbuild-build-depends-htslib-dummy' in '/<<BUILDDIR>>/resolver-ZwYIUu/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-ZwYIUu/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ZwYIUu/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ZwYIUu/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ZwYIUu/apt_archive ./ Sources [538 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ZwYIUu/apt_archive ./ Packages [622 B]
Fetched 2493 B in 1s (3328 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev debhelper dh-autoreconf dh-exec
  dh-strip-nondeterminism dwz file gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcroco3
  libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
  libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0
  libgssapi-krb5-2 libicu67 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
  libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1
  libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf
  zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
  libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
  libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config
  krb5-doc krb5-user liblzma-doc libssl-doc libtool-doc gfortran
  | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
  libmail-box-perl
Recommended packages:
  curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
  libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix
  libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev debhelper dh-autoreconf dh-exec
  dh-strip-nondeterminism dwz file gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcroco3
  libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
  libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0
  libgssapi-krb5-2 libicu67 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
  libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1
  libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf
  sbuild-build-depends-htslib-dummy zlib1g-dev
0 upgraded, 52 newly installed, 0 to remove and 19 not upgraded.
Need to get 22.4 MB/23.6 MB of archives.
After this operation, 83.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ZwYIUu/apt_archive ./ sbuild-build-depends-htslib-dummy 0.invalid.0 [908 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.180-1 [162 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.4-1 [1159 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-3 [8287 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf dh-exec armhf 0.23.2+b3 [25.7 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-7 [258 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-10+b3 [62.0 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-10+b3 [112 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-10+b3 [318 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-10+b3 [135 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.41.0-2 [61.2 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.68.0-1+b1 [285 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.68.0-1+b1 [358 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.6-1 [40.8 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1g-1 [1573 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libkrb5-3:armhf (1.17-10+b3) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../39-libgssapi-krb5-2_1.17-10+b3_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.17-10+b3) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../40-libnghttp2-14_1.41.0-2_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.41.0-2) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../41-libpsl5_0.21.0-1.1_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1.1) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../42-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../43-libssh2-1_1.8.0-2.1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-2.1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../44-libcurl3-gnutls_7.68.0-1+b1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.68.0-1+b1) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
Preparing to unpack .../45-libcurl4-gnutls-dev_7.68.0-1+b1_armhf.deb ...
Unpacking libcurl4-gnutls-dev:armhf (7.68.0-1+b1) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../46-libdeflate0_1.6-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.6-1) ...
Selecting previously unselected package libdeflate-dev:armhf.
Preparing to unpack .../47-libdeflate-dev_1.6-1_armhf.deb ...
Unpacking libdeflate-dev:armhf (1.6-1) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../48-liblzma-dev_5.2.4-1_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.4-1) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../49-libssl-dev_1.1.1g-1_armhf.deb ...
Unpacking libssl-dev:armhf (1.1.1g-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../50-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-htslib-dummy.
Preparing to unpack .../51-sbuild-build-depends-htslib-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.21.0-1.1) ...
Setting up libicu67:armhf (67.1-3) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.4-1) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1g-1) ...
Setting up libdebhelper-perl (13.2) ...
Setting up libbrotli1:armhf (1.0.7-7) ...
Setting up libnghttp2-14:armhf (1.41.0-2) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up libdeflate0:armhf (1.6-1) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up libkrb5support0:armhf (1.17-10+b3) ...
Setting up autotools-dev (20180224.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libssl-dev:armhf (1.1.1g-1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libk5crypto3:armhf (1.17-10+b3) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-10+b3) ...
Setting up libdeflate-dev:armhf (1.6-1) ...
Setting up libelf1:armhf (0.180-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-5+b1) ...
Setting up libbz2-dev:armhf (1.0.8-4) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
Setting up libgssapi-krb5-2:armhf (1.17-10+b3) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up automake (1:1.16.2-3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up libcurl3-gnutls:armhf (7.68.0-1+b1) ...
Setting up libcurl4-gnutls-dev:armhf (7.68.0-1+b1) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up debhelper (13.2) ...
Setting up dh-exec (0.23.2+b3) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34.90.20200706-1+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-15+rpi1 gcc-9_9.3.0-15+rpi1 libc6-dev_2.31-2+rpi1 libstdc++-9-dev_9.3.0-15+rpi1 libstdc++6_10.1.0-6+rpi1 linux-libc-dev_5.7.6-1+rpi1
Package versions: adduser_3.118 apt_2.1.7 aptitude_0.8.13-1+b1 aptitude-common_0.8.13-1 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34.90.20200706-1+rpi1 binutils-arm-linux-gnueabihf_2.34.90.20200706-1+rpi1 binutils-common_2.34.90.20200706-1+rpi1 bsdextrautils_2.36-1 bsdutils_1:2.36-1 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-15+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-exec_0.23.2+b3 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.36-1 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-15+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-6+rpi1 gcc-9_9.3.0-15+rpi1 gcc-9-base_9.3.0-15+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.7 libarchive-zip-perl_1.68-1 libasan5_9.3.0-15+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-6+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34.90.20200706-1+rpi1 libblkid1_2.36-1 libboost-iostreams1.71.0_1.71.0-6+b1 libbrotli1_1.0.7-7 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-2+rpi1 libc-dev-bin_2.31-2+rpi1 libc6_2.31-2+rpi1 libc6-dev_2.31-2+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcap2-bin_1:2.36-1 libcc1-0_10.1.0-6+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34.90.20200706-1+rpi1 libctf0_2.34.90.20200706-1+rpi1 libcurl3-gnutls_7.68.0-1+b1 libcurl4-gnutls-dev_7.68.0-1+b1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2 libdeflate-dev_1.6-1 libdeflate0_1.6-1 libdpkg-perl_1.19.7 libelf1_0.180-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.36-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-15+rpi1 libgcc-s1_10.1.0-6+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.1.0-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libhogweed6_3.6-2 libicu67_67.1-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 libldap-2.4-2_2.4.50+dfsg-1+b1 libldap-common_2.4.50+dfsg-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1 libpam-cap_1:2.36-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libpsl5_0.21.0-1.1 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.2-1 libsigsegv2_2.12-2 libsmartcols1_2.36-1 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1g-1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-15+rpi1 libstdc++6_10.1.0-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1+b1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-6+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1+b1 libunistring2_0.9.10-4 libuuid1_2.36-1 libxapian30_1.4.15-1 libxml2_2.9.10+dfsg-5+b1 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.7.6-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-1 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

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


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

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Aug  3 11:38:53 2020 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_1.10.2-5.dsc
dpkg-source: info: extracting htslib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking htslib_1.10.2.orig.tar.bz2
dpkg-source: info: unpacking htslib_1.10.2-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying no_git_version
dpkg-source: info: applying define_PATH_MAX.patch
dpkg-source: info: applying fPIC.patch
dpkg-source: info: applying testShebang.patch
dpkg-source: info: applying fix_float_precision
dpkg-source: info: applying big-endian
dpkg-source: info: applying cram_to_bam_export.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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-8aee64db-bd41-4514-bed2-f7c3c9d40917
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 1.10.2-5
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from htslib-1.10.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
	install -d /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home
	make -j4 distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.tmp test/*.tmp.* test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* header-exports.txt shlib-exports-so.txt
rm -f libhts.so libhts.so.*
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f hts-object-files
rm -f libhts.a bgzip htsfile tabix  test/hts_endian test/fieldarith test/hfile test/pileup test/sam test/test_bgzf test/test_kstring test/test_realn test/test-regidx test/test_str2int test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk
rm -rf autom4te.cache
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -rf test_backup/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files
	rm -fr -- debian/libhts3/ debian/tmp/ debian/libhts-dev/ debian/htslib-test/ debian/tabix/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
	find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a  -type f -exec md5sum {} + -o -type l -printf "symlink  %p
" > debian/autoreconf.before
	grep -q ^XDT_ configure.ac
	autoreconf -f -i
	find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a  -type f -exec md5sum {} + -o -type l -printf "symlink  %p
" > debian/autoreconf.after
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# create clean copy of test dir
cp -a test test_backup
# to help with cross building, otherwise MMAP might get turned off
export ac_cv_func_mmap_fixed_mapped=yes && autoconf && \
dh_auto_configure -- --enable-libcurl --enable-gcs --enable-s3
	install -d /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home
	./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for pkg-config... no
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 for unknown-Linux... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... (cached) yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for libdeflate.h... yes
checking for libdeflate_deflate_compress in -ldeflate... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
	rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
   debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- \
  CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
  CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
  LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
  PACKAGE_VERSION="1.10.2-5" \
  libdir=/usr/lib/arm-linux-gnueabihf
	make -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.10.2-5 libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION_TEXT "1.10.2-5"' > version.h
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_libcurl.o hfile_libcurl.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_gcs.o hfile_gcs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_s3.o hfile_s3.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_s3_write.o hfile_s3_write.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o knetfile.pico knetfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_net.pico hfile_net.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
gcc -shared -Wl,-soname,libhts.so.3 -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.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/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/string_alloc.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/hts_endian test/hts_endian.o -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_str2int test/test_str2int.o
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.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/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o   hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o
ranlib libhts.a
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
ln -sf libhts.so libhts.so.3
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -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/libhts3.debhelper.log debian/tabix.debhelper.log
   debian/rules override_dh_auto_test-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -- \
  CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
  CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
  LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
  PACKAGE_VERSION="1.10.2-5" \
  libdir=/usr/lib/arm-linux-gnueabihf \
  || \
  if find . -name "FAIL*" > /dev/null ; then \
    for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \
  fi
	make -j4 test VERBOSE=1 "CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.10.2-5 libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<PKGBUILDDIR>>'
test/hts_endian
test/test_kstring
test/test_str2int
test/fieldarith test/fieldarith.sam
test/hfile
test/test_bgzf test/bgziptest.txt
test/test-parse-reg -t test/colons.bam
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead
Expected error: [E::hts_parse_region] Mismatching braces in "{chr1"
Expected error: [E::hts_parse_region] Unexpected string "x" after region
Expected error: [E::hts_parse_region] Unexpected string "y" after region
Expected error: [E::hts_parse_region] Unexpected string "chr3" after region
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
cd test/mpileup && ./test-pileup.sh mpileup.tst
Testing (m)pileup...
PASS : $pileup mp_D.sam
PASS : $pileup -m mp_D.sam
PASS : $pileup mp_DI.sam
PASS : $pileup -m mp_DI.sam
PASS : $pileup mp_I.sam
PASS : $pileup -m mp_I.sam
PASS : $pileup mp_P.sam
PASS : $pileup -m mp_P.sam
PASS : $pileup mp_ID.sam
PASS : $pileup -m mp_ID.sam
PASS : $pileup mp_N.sam
PASS : $pileup -m mp_N.sam
PASS : $pileup mp_N2.sam
PASS : $pileup -m mp_N2.sam
PASS : $pileup c1#pad1.sam
PASS : $pileup -m c1#pad1.sam
PASS : $pileup c1#pad2.sam
PASS : $pileup -m c1#pad2.sam
PASS : $pileup c1#pad3.sam
PASS : $pileup -m c1#pad3.sam
PASS : $pileup -m small.bam

Expected   passes:   21
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq
test/test-regidx
cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-}
bgzip round-trip no threads: .. ok

bgzip -b no threads: .. ok

bgzip -b -I no threads: .. ok

bgzip round-trip  4 threads: .. ok

bgzip -b  4 threads: .. ok

bgzip -b -I  4 threads: .. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view  -l 0 -b -m 14 -x /tmp/h5xbixJ3ux/index.bam.csi /<<PKGBUILDDIR>>/test/index.sam > /tmp/h5xbixJ3ux/index.bam
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -c /tmp/h5xbixJ3ux/index.bam
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view  -l 0 -b -m 0 -x /tmp/h5xbixJ3ux/index.bam.bai /<<PKGBUILDDIR>>/test/index.sam > /tmp/h5xbixJ3ux/index.bam
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -b /tmp/h5xbixJ3ux/index.bam
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view  -l 0 -z -m 14 -x /tmp/h5xbixJ3ux/index.sam.gz.csi /<<PKGBUILDDIR>>/test/index.sam > /tmp/h5xbixJ3ux/index.sam.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -c /tmp/h5xbixJ3ux/index.sam.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view  -l 0 -z -m 0 -x /tmp/h5xbixJ3ux/index.sam.gz.bai /<<PKGBUILDDIR>>/test/index.sam > /tmp/h5xbixJ3ux/index.sam.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -b /tmp/h5xbixJ3ux/index.sam.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view  -l 0 -C -x /tmp/h5xbixJ3ux/index.cram.crai /<<PKGBUILDDIR>>/test/index.sam > /tmp/h5xbixJ3ux/index.cram
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index /tmp/h5xbixJ3ux/index.cram
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view  -l 0 -b -m 14 -x /tmp/h5xbixJ3ux/index.bcf.csi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/h5xbixJ3ux/index.bcf
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -c /tmp/h5xbixJ3ux/index.bcf
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view  -l 0 -z -m 14 -x /tmp/h5xbixJ3ux/index.vcf.gz.csi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/h5xbixJ3ux/index.vcf.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -c /tmp/h5xbixJ3ux/index.vcf.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view  -l 0 -z -m 0 -x /tmp/h5xbixJ3ux/index.vcf.gz.tbi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/h5xbixJ3ux/index.vcf.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -t /tmp/h5xbixJ3ux/index.vcf.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/tabix /tmp/h5xbixJ3ux/index.vcf.gz##idx##/tmp/h5xbixJ3ux/index.vcf.gz.tbi 1:10000060-10000060
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/h5xbixJ3ux/index.bam.csi /<<PKGBUILDDIR>>/test/index.sam > /tmp/h5xbixJ3ux/index.bam
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -c /tmp/h5xbixJ3ux/index.bam
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -b -m 0 -x /tmp/h5xbixJ3ux/index.bam.bai /<<PKGBUILDDIR>>/test/index.sam > /tmp/h5xbixJ3ux/index.bam
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -b /tmp/h5xbixJ3ux/index.bam
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/h5xbixJ3ux/index.sam.gz.csi /<<PKGBUILDDIR>>/test/index.sam > /tmp/h5xbixJ3ux/index.sam.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -c /tmp/h5xbixJ3ux/index.sam.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/h5xbixJ3ux/index.sam.gz.bai /<<PKGBUILDDIR>>/test/index.sam > /tmp/h5xbixJ3ux/index.sam.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -b /tmp/h5xbixJ3ux/index.sam.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -C -x /tmp/h5xbixJ3ux/index.cram.crai /<<PKGBUILDDIR>>/test/index.sam > /tmp/h5xbixJ3ux/index.cram
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index /tmp/h5xbixJ3ux/index.cram
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/h5xbixJ3ux/index.bcf.csi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/h5xbixJ3ux/index.bcf
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -c /tmp/h5xbixJ3ux/index.bcf
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/h5xbixJ3ux/index.vcf.gz.csi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/h5xbixJ3ux/index.vcf.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -c /tmp/h5xbixJ3ux/index.vcf.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/h5xbixJ3ux/index.vcf.gz.tbi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/h5xbixJ3ux/index.vcf.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/test/test_index -t /tmp/h5xbixJ3ux/index.vcf.gz
.. ok

test_index:
	/<<PKGBUILDDIR>>/tabix /tmp/h5xbixJ3ux/index.vcf.gz##idx##/tmp/h5xbixJ3ux/index.vcf.gz.tbi 1:10000060-10000060
.. ok

test_view testing multi-ref CRAM modes:
  ./test_view  -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view  multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
  ./test_view  -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view  multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
  ./test_view  -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view  multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok

test_view testing multi-ref CRAM modes:
  ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
  ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
  ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

test_view testing xx#MD2.sam, ref xx.fa:
  ./test_view  -S -b xx#MD2.sam > xx#MD2.tmp.bam
  ./test_view  xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
  ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
  ./test_view  -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
  ./test_view  xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
  ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view  -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
  ./test_view  -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
  ./test_view  xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view  -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
  ./test_view  -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
  ./test_view  xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
  ./test_view  -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
  ./test_view  -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
  ./test_view  xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
.. ok

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

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

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

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

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

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

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

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

test_view testing region queries:
  ./test_view  -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
  ./test_view  range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
.. ok

test_view testing BAM files with absent @SQ lines:
  ./test_view  -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
  ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
  ./test_view  -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
  ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok

test_view testing large (> 2Gbases) positions:
  ./test_view  -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
  ./test_view  -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
  ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
	/<<PKGBUILDDIR>>/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok

  ./test_view  -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
  ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
  ./test_view  -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
  ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.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 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam
  ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
  ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
  ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram
  ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view -@4 -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
  ./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
  ./test_view -@4 auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t auxf.fa -S -l0 -C -o VERSION=3.0 auxf#values.sam > auxf#values.tmp.cram
  ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
  ./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
  ./test_view -@4 auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
  ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
  ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
  ./test_view -@4 auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_
  ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

test_view testing xx#MD2.sam, ref xx.fa:
  ./test_view -@4 -S -b xx#MD2.sam > xx#MD2.tmp.bam
  ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
  ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
  ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
  ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
  ./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
  ./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
  ./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
  ./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
  ./test_view -@4 xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
.. ok

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

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

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

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

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

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

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

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

test_view testing region queries:
  ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
  ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
.. ok

test_view testing BAM files with absent @SQ lines:
  ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
  ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
  ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
  ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok

test_view testing large (> 2Gbases) positions:
  ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
  ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
  ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
	/<<PKGBUILDDIR>>/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok

  ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
  ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
  ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
  ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam
.. ok


test_MD testing xx#MD.sam, ref xx.fa:
  ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
  ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
  ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_
  ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
  ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
  ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_
  Checking for MD/NM in xx#MD.sam
  ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
  ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
  ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_
.. ok


test_MD testing xx#MD2.sam, ref xx.fa:
  ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_
  ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_
  ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_
.. ok

test_vcf_api:
	/<<PKGBUILDDIR>>/test/test-vcf-api /tmp/h5xbixJ3ux/test-vcf-api.bcf
[E::bcf_index_build3] TBI indices for BCF files are not supported
[E::idx_find_and_load] Could not retrieve index file for '/tmp/h5xbixJ3ux/test-vcf-api.bcf'
.. ok

test_vcf_sweep:
	/<<PKGBUILDDIR>>/test/test-vcf-sweep /tmp/h5xbixJ3ux/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/h5xbixJ3ux -s 1274967582
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/h5xbixJ3ux -s 310698583
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/h5xbixJ3ux -s 1160709743
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/h5xbixJ3ux -s 1546831053
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/h5xbixJ3ux -s 1020066187
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/h5xbixJ3ux -s 876229045
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/h5xbixJ3ux -s 943203484
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/h5xbixJ3ux -s 338069
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/h5xbixJ3ux -s 70805941
.. ok

test-bcf-sr:
	/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/h5xbixJ3ux -s 1062375311
.. ok

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

test_convert_padded_header:
	/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/h5xbixJ3ux/headernul0.bam
.. ok

test_convert_padded_header:
	/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/h5xbixJ3ux/headernul1.bam
.. ok

test_convert_padded_header:
	/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/h5xbixJ3ux/headernul678.bam
.. ok

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

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

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

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

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

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

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

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

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

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

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


Number of tests:
    total   .. 153
    passed  .. 153
    failed  .. 0

make[2]: Leaving directory '/<<PKGBUILDDIR>>'
	rm -fr -- /tmp/dh-xdg-rundir-YXMBPjAF
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_testroot -a
   dh_prep -a
	rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/tabix.substvars
	rm -fr -- debian/.debhelper/generated/libhts3/ debian/libhts3/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/tabix/ debian/tabix/
	rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
   debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \
    rm /<<PKGBUILDDIR>>/test/${binary} ; \
done
dh_auto_install -- prefix=/usr \
  CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
  CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
  LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
  PACKAGE_VERSION="1.10.2-5" \
  libdir=/usr/lib/arm-linux-gnueabihf
	install -d /<<PKGBUILDDIR>>/debian/tmp
	make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.10.2-5 libdir=/usr/lib/arm-linux-gnueabihf
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/share/man/man7 /<<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.1.10.2-5
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.10.2-5#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.1.10.2-5 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so
ln -sf libhts.so.1.10.2-5 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3
install -p bgzip htsfile tabix /<<PKGBUILDDIR>>/debian/tmp/usr/bin
if test -n ""; then install -p  /<<PKGBUILDDIR>>/debian/tmp; fi
install -p -m 644 htslib/*.h /<<PKGBUILDDIR>>/debian/tmp/usr/include/htslib
install -p -m 644 libhts.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a
install -p -m 644 bgzip.1 htsfile.1 tabix.1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man5
install -p -m 644 htslib-s3-plugin.7 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man7
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# restore clean copy of test dir before dh_install is run
# This should not be done earlier since dh_auto_install contains some unconditional removals
rm -f -r test
mv test_backup test
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install -a
	install -d debian/libhts3/usr/lib/arm-linux-gnueabihf
	cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.10.2-5 debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3 debian/libhts3/usr/lib/arm-linux-gnueabihf/
	install -d debian/.debhelper/generated/libhts3
	install -d debian/libhts-dev/usr/include
	cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/
	install -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf
	cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so debian/libhts-dev/usr/lib/arm-linux-gnueabihf/
	install -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
	cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig/
	install -d debian/libhts-dev/usr/share/man/man5
	cp --reflink=auto -a debian/tmp/usr/share/man/man5/faidx.5 debian/tmp/usr/share/man/man5/sam.5 debian/tmp/usr/share/man/man5/vcf.5 debian/libhts-dev/usr/share/man/man5/
	install -d debian/.debhelper/generated/libhts-dev
	install -d debian/.debhelper/generated/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
	rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
   debian/rules override_dh_installdocs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installdocs
	install -d debian/libhts3/usr/share/doc/libhts3
	install -p -m0644 debian/copyright debian/libhts3/usr/share/doc/libhts3/copyright
	install -d debian/libhts-dev/usr/share/doc/libhts-dev
	cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev
	cp --reflink=auto -a ./README debian/libhts-dev/usr/share/doc/libhts-dev
	cp --reflink=auto -a ./README.large_positions.md debian/libhts-dev/usr/share/doc/libhts-dev
	chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc
	install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright
	install -d debian/tabix/usr/share/doc/tabix
	install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright
# Fix Perl interpreter path
for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
    sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
grep: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so: No such file or directory
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
	rm -f debian/libhts-dev.debhelper.log debian/libhts3.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/libhts3/usr/share/doc/libhts3/changelog.Debian
	install -p -m0644 NEWS debian/libhts3/usr/share/doc/libhts3/changelog
	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
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installman -a
	install -d debian/libhts3/usr/share/man/man7/
	install -p -m0644 ./htslib-s3-plugin.7 debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
	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
	install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 debian/libhts-dev/usr/share/man/man5/faidx.5
	man-recode --to-code UTF-8 --suffix .dh-new debian/libhts-dev/usr/share/man/man5/sam.5 debian/libhts-dev/usr/share/man/man5/vcf.5
	man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/tabix.1
	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/sam.5.dh-new debian/libhts-dev/usr/share/man/man5/sam.5
	mv debian/libhts-dev/usr/share/man/man5/vcf.5.dh-new debian/libhts-dev/usr/share/man/man5/vcf.5
	chmod 0644 -- debian/libhts-dev/usr/share/man/man5/sam.5 debian/libhts-dev/usr/share/man/man5/vcf.5
	mv debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
	mv debian/libhts-dev/usr/share/man/man5/faidx.5.dh-new debian/libhts-dev/usr/share/man/man5/faidx.5
	chmod 0644 -- debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 debian/libhts-dev/usr/share/man/man5/faidx.5
	mv debian/tabix/usr/share/man/man1/bgzip.1.dh-new debian/tabix/usr/share/man/man1/bgzip.1
	mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1
	chmod 0644 -- debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1
   dh_perl -a
   dh_link -a
	rm -f debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.3
	ln -s libhts.so.1.10.2-5 debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.3
	rm -f debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
	ln -s libhts.so.1.10.2-5 debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
	rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz
	ln -s tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz
   dh_strip_nondeterminism -a
   dh_compress -a
	cd debian/libhts3
	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/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
	chmod a-x usr/share/doc/libhts-dev/README.large_positions.md 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/libhts3/changelog usr/share/doc/libhts3/changelog.Debian usr/share/man/man7/htslib-s3-plugin.7
	gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
	gzip -9nf usr/share/doc/libhts3/changelog usr/share/doc/libhts3/changelog.Debian usr/share/man/man7/htslib-s3-plugin.7
	gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5
	cd '/<<PKGBUILDDIR>>'
	cd '/<<PKGBUILDDIR>>'
	cd '/<<PKGBUILDDIR>>'
	rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
   debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
	find debian/libhts3 ! -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 ! -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/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/libhts3/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3/usr/share/doc/[^/]*/examples/.*' -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/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/libhts3/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	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/libhts3/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhts3 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
	find debian/libhts3/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
find debian -name simple_test_driver.sh -exec chmod +x \{\} \;
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
	rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
   debian/rules override_dh_missing
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# FIXME: No idea why these files are remaining in debian/tmp
rm -rf debian/tmp/usr/bin debian/tmp/usr/share/man
dh_missing
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_dwz -a -a
	dwz -- debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.10.2-5
	install -d debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf
	dwz -mdebian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix
	objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug
	rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
   debian/rules override_dh_strip
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# This is apparently important for the interpretation by ldc2 in sambamba
dh_strip -Xlibhts.a
	install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/c4
	objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.10.2-5 debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/c4/e3b5795941af46dfeb67dee3f0d3b55e539730.debug
	install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c1
	objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c1/b922c33a7f751f646b1b572100d151c9f31d37.debug
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c1/b922c33a7f751f646b1b572100d151c9f31d37.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/c1/b922c33a7f751f646b1b572100d151c9f31d37.debug debian/tabix/usr/bin/bgzip
	install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be
	objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be/3d87f407c881bd8dc5fa76a128c8a4f5ac4a74.debug
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be/3d87f407c881bd8dc5fa76a128c8a4f5ac4a74.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/be/3d87f407c881bd8dc5fa76a128c8a4f5ac4a74.debug debian/tabix/usr/bin/htsfile
	install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/16
	objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/16/c3baf77adf0c7d598684e024b9a389d471655b.debug
	chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/c4/e3b5795941af46dfeb67dee3f0d3b55e539730.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.10.2-5
	objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/c4/e3b5795941af46dfeb67dee3f0d3b55e539730.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.10.2-5
	install -d debian/.debhelper/libhts3/dbgsym-root/usr/share/doc
	ln -s libhts3 debian/.debhelper/libhts3/dbgsym-root/usr/share/doc/libhts3-dbgsym
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/16/c3baf77adf0c7d598684e024b9a389d471655b.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/16/c3baf77adf0c7d598684e024b9a389d471655b.debug debian/tabix/usr/bin/tabix
	install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz
	cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz
	rm -fr debian/tabix/usr/lib/debug/.dwz
	rmdir -p --ignore-fail-on-non-empty debian/tabix/usr/lib/debug
	install -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc
	ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_makeshlibs -a -a
	rm -f debian/libhts3/DEBIAN/shlibs
	install -d debian/libhts3/DEBIAN
	echo "libhts 3 libhts3 (>= 1.10.2)" >> debian/libhts3/DEBIAN/shlibs
	chmod 0644 -- debian/libhts3/DEBIAN/shlibs
	dpkg-gensymbols -plibhts3 -Idebian/libhts3.symbols -Pdebian/libhts3 -edebian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.10.2-5
	mv debian/.debhelper/generated/libhts3/triggers.new debian/.debhelper/generated/libhts3/triggers
	rm -f debian/libhts-dev/DEBIAN/shlibs
	rm -f debian/tabix/DEBIAN/shlibs
   dh_shlibdeps -a -a
	dpkg-shlibdeps -Tdebian/libhts3.substvars debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.10.2-5
	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/htsfile debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/tabix were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
   dh_installdeb -a
	install -p -m0644 debian/.debhelper/generated/libhts3/triggers debian/libhts3/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/libhts3.substvars
	echo misc:Pre-Depends= >> debian/libhts3.substvars
	install -d debian/.debhelper/libhts3/dbgsym-root/DEBIAN
	dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/.debhelper/libhts3/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=libhts3-dbgsym "-DDepends=libhts3 (= \${binary:Version})" "-DDescription=debug symbols for libhts3" -DBuild-Ids=c4e3b5795941af46dfeb67dee3f0d3b55e539730 -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 -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=16c3baf77adf0c7d598684e024b9a389d471655b be3d87f407c881bd8dc5fa76a128c8a4f5ac4a74 c1b922c33a7f751f646b1b572100d151c9f31d37" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
	chmod 0644 -- debian/libhts-dev/DEBIAN/control
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix
	chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/libhts3
	chmod 0644 -- debian/libhts3/DEBIAN/control
	chmod 0644 -- debian/tabix/DEBIAN/control
   dh_md5sums -a
	cd debian/libhts3 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/libhts3/DEBIAN/md5sums
	chmod 0644 -- debian/tabix/DEBIAN/md5sums
	cd debian/.debhelper/libhts3/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/md5sums
	chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums
   dh_builddeb -a
	dpkg-deb --root-owner-group --build debian/libhts3 ..
	dpkg-deb --root-owner-group --build debian/libhts-dev ..
	dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root ..
dpkg-deb: building package 'libhts3' in '../libhts3_1.10.2-5_armhf.deb'.
dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.10.2-5_armhf.deb'.
dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.10.2-5_armhf.deb'.
	dpkg-deb --root-owner-group --build debian/.debhelper/libhts3/dbgsym-root ..
dpkg-deb: building package 'libhts3-dbgsym' in '../libhts3-dbgsym_1.10.2-5_armhf.deb'.
	dpkg-deb --root-owner-group --build debian/tabix ..
dpkg-deb: building package 'tabix' in '../tabix_1.10.2-5_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../htslib_1.10.2-5_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-source: info: using options from htslib-1.10.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-08-05T05:30:53Z

Finished
--------

I: Built successfully

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


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


htslib_1.10.2-5_armhf.changes:
------------------------------

Format: 1.8
Date: Mon, 03 Aug 2020 13:19:08 +0200
Source: htslib
Binary: libhts-dev libhts3 libhts3-dbgsym tabix tabix-dbgsym
Architecture: armhf
Version: 1.10.2-5
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 libhts-dev - development files for the HTSlib
 libhts3    - C library for high-throughput sequencing data formats
 tabix      - generic indexer for TAB-delimited genome position files
Changes:
 htslib (1.10.2-5) unstable; urgency=medium
 .
   * debhelper-compat 13 (routine-update)
   * Add salsa-ci file (routine-update)
   * Remove default debian/gbp.conf
   * Install bgzip.1 manpage
   * Workaround issue with dh_missing
Checksums-Sha1:
 986f7a91b8a9bf6b870c97b393f27de22b093304 6229 htslib_1.10.2-5_armhf.buildinfo
 1a87861292e822561744fa41e7d1bff04df3cf3c 4795628 libhts-dev_1.10.2-5_armhf.deb
 8222dbe119840b279afab452dbcb9eebf24d00d2 1054316 libhts3-dbgsym_1.10.2-5_armhf.deb
 38b9c3fa94b91eff817f407d0010f8cb6545cc71 320748 libhts3_1.10.2-5_armhf.deb
 d90f4f81c325a833c9a41c5ab857a426bfc96aee 1579556 tabix-dbgsym_1.10.2-5_armhf.deb
 552696a4ee592f287832f7ef69e2be0e67deb53c 319428 tabix_1.10.2-5_armhf.deb
Checksums-Sha256:
 f16c0861698755ea1da186cf30fefed025715568bcd92364953dad27f3de3420 6229 htslib_1.10.2-5_armhf.buildinfo
 fb07d08b673ba4d4332c039f1e81ce4bb1eb2a1db067c8e53733446468c5e973 4795628 libhts-dev_1.10.2-5_armhf.deb
 dcf646149c5b8a2c93cd9f1503940cf15f3be7d329a4c6cd57d5b3f5b37505b9 1054316 libhts3-dbgsym_1.10.2-5_armhf.deb
 0a320325915601546a5c128cee0622e0b56b5f0a059bf4907ce784836e0868b7 320748 libhts3_1.10.2-5_armhf.deb
 215b160bf0e6df5eac264f2661dd6dc58c24d5fd993ec30b6411816ad37c8a94 1579556 tabix-dbgsym_1.10.2-5_armhf.deb
 c769ede5cbec416342f9677992addc793c34c78b92f9f2714ee340c7aef9b4be 319428 tabix_1.10.2-5_armhf.deb
Files:
 3db12ad424f00a92a76f071e6b2456ba 6229 science optional htslib_1.10.2-5_armhf.buildinfo
 690df5d25b5577b4ac683d94f3a9de18 4795628 libdevel optional libhts-dev_1.10.2-5_armhf.deb
 44191757fad27bfa030213894203bd76 1054316 debug optional libhts3-dbgsym_1.10.2-5_armhf.deb
 98173769f2d64716fdaa7edf7ed0c661 320748 libs optional libhts3_1.10.2-5_armhf.deb
 0a3761a4ef682dfaf9233ce114497e14 1579556 debug optional tabix-dbgsym_1.10.2-5_armhf.deb
 9d52c5a18bd3fd6aaa31b2a57d1b1cbd 319428 science optional tabix_1.10.2-5_armhf.deb

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


libhts-dev_1.10.2-5_armhf.deb
-----------------------------

 new Debian package, version 2.0.
 size 4795628 bytes: control archive=2000 bytes.
    1174 bytes,    27 lines      control              
    2413 bytes,    37 lines      md5sums              
 Package: libhts-dev
 Source: htslib
 Version: 1.10.2-5
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5822
 Depends: libhts3 (= 1.10.2-5), liblzma-dev, zlib1g-dev
 Section: libdevel
 Priority: optional
 Multi-Arch: same
 Homepage: https://github.com/samtools/htslib
 Description: development files for the HTSlib
  HTSlib is an implementation of a unified C library for accessing common file
  formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
  Format), used for high-throughput sequencing data, and is the core library
  used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
  compatible with gcc, g++ and clang.
  .
  HTSlib implements a generalized BAM (binary SAM) index, with file extension
  ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
  new index and then for the old if the new index is absent.
  .
  This package contains development files for the HTSlib: headers, static
  library, manual pages, etc.
  .
  For compatibility with sambamba, the internal routine cram_to_bam was
  exported, hereto adopting a patch found in guix.

drwxr-xr-x root/root         0 2020-08-03 11:19 ./
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/include/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/include/htslib/
-rw-r--r-- root/root     16101 2019-11-19 11:20 ./usr/include/htslib/bgzf.h
-rw-r--r-- root/root     15928 2019-11-26 21:07 ./usr/include/htslib/cram.h
-rw-r--r-- root/root     12245 2019-11-26 21:07 ./usr/include/htslib/faidx.h
-rw-r--r-- root/root     10979 2019-11-19 11:20 ./usr/include/htslib/hfile.h
-rw-r--r-- root/root     48171 2019-12-19 09:52 ./usr/include/htslib/hts.h
-rw-r--r-- root/root      3889 2019-11-19 11:20 ./usr/include/htslib/hts_defs.h
-rw-r--r-- root/root     11446 2017-09-27 15:40 ./usr/include/htslib/hts_endian.h
-rw-r--r-- root/root      3944 2019-10-01 22:06 ./usr/include/htslib/hts_log.h
-rw-r--r-- root/root      2124 2019-11-19 11:20 ./usr/include/htslib/hts_os.h
-rw-r--r-- root/root      5603 2019-11-19 11:20 ./usr/include/htslib/kbitset.h
-rw-r--r-- root/root      2828 2019-11-19 11:20 ./usr/include/htslib/kfunc.h
-rw-r--r-- root/root     22882 2019-11-19 11:20 ./usr/include/htslib/khash.h
-rw-r--r-- root/root      3995 2019-11-19 11:20 ./usr/include/htslib/khash_str2int.h
-rw-r--r-- root/root      5135 2019-11-19 11:20 ./usr/include/htslib/klist.h
-rw-r--r-- root/root      2972 2019-11-19 11:20 ./usr/include/htslib/knetfile.h
-rw-r--r-- root/root      9186 2019-11-19 11:20 ./usr/include/htslib/kseq.h
-rw-r--r-- root/root     11480 2019-11-19 11:20 ./usr/include/htslib/ksort.h
-rw-r--r-- root/root     11416 2019-12-06 12:42 ./usr/include/htslib/kstring.h
-rw-r--r-- root/root      8913 2019-11-26 21:07 ./usr/include/htslib/regidx.h
-rw-r--r-- root/root     67260 2019-11-26 21:07 ./usr/include/htslib/sam.h
-rw-r--r-- root/root     15605 2019-11-26 21:07 ./usr/include/htslib/synced_bcf_reader.h
-rw-r--r-- root/root      4925 2019-11-26 21:07 ./usr/include/htslib/tbx.h
-rw-r--r-- root/root     12492 2019-11-26 21:07 ./usr/include/htslib/thread_pool.h
-rw-r--r-- root/root     59787 2020-08-03 11:19 ./usr/include/htslib/vcf.h
-rw-r--r-- root/root      1681 2019-11-19 11:20 ./usr/include/htslib/vcf_sweep.h
-rw-r--r-- root/root      4925 2019-10-01 22:06 ./usr/include/htslib/vcfutils.h
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root   5516504 2020-08-03 11:19 ./usr/lib/arm-linux-gnueabihf/libhts.a
lrwxrwxrwx root/root         0 2020-08-03 11:19 ./usr/lib/arm-linux-gnueabihf/libhts.so -> libhts.so.1.10.2-5
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root       628 2020-08-03 11:19 ./usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/doc/libhts-dev/
-rw-r--r-- root/root       273 2014-08-15 09:12 ./usr/share/doc/libhts-dev/README
-rw-r--r-- root/root      2961 2019-12-10 17:59 ./usr/share/doc/libhts-dev/README.large_positions.md.gz
-rw-r--r-- root/root       401 2020-08-03 11:19 ./usr/share/doc/libhts-dev/README.test
-rw-r--r-- root/root      5339 2020-08-03 11:19 ./usr/share/doc/libhts-dev/changelog.Debian.gz
-rw-r--r-- root/root     15663 2019-12-19 09:52 ./usr/share/doc/libhts-dev/changelog.gz
-rw-r--r-- root/root      5817 2020-08-03 11:19 ./usr/share/doc/libhts-dev/copyright
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/man/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/man/man5/
-rw-r--r-- root/root      2452 2020-08-03 11:19 ./usr/share/man/man5/faidx.5.gz
-rw-r--r-- root/root      1539 2020-08-03 11:19 ./usr/share/man/man5/sam.5.gz
-rw-r--r-- root/root      1857 2020-08-03 11:19 ./usr/share/man/man5/vcf.5.gz


libhts3-dbgsym_1.10.2-5_armhf.deb
---------------------------------

 new Debian package, version 2.0.
 size 1054316 bytes: control archive=556 bytes.
     389 bytes,    13 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: libhts3-dbgsym
 Source: htslib
 Version: 1.10.2-5
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1129
 Depends: libhts3 (= 1.10.2-5)
 Section: debug
 Priority: optional
 Multi-Arch: same
 Description: debug symbols for libhts3
 Build-Ids: c4e3b5795941af46dfeb67dee3f0d3b55e539730

drwxr-xr-x root/root         0 2020-08-03 11:19 ./
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/debug/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/debug/.build-id/c4/
-rw-r--r-- root/root   1145844 2020-08-03 11:19 ./usr/lib/debug/.build-id/c4/e3b5795941af46dfeb67dee3f0d3b55e539730.debug
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-08-03 11:19 ./usr/share/doc/libhts3-dbgsym -> libhts3


libhts3_1.10.2-5_armhf.deb
--------------------------

 new Debian package, version 2.0.
 size 320748 bytes: control archive=3652 bytes.
    1153 bytes,    22 lines      control              
     367 bytes,     5 lines      md5sums              
      29 bytes,     1 lines      shlibs               
   14024 bytes,   525 lines      symbols              
      65 bytes,     2 lines      triggers             
 Package: libhts3
 Source: htslib
 Version: 1.10.2-5
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 775
 Depends: libbz2-1.0, libc6 (>= 2.29), libcurl3-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0)
 Breaks: libtabixpp (<< 1.0.0-5~), python-pysam (<< 0.15~), python3-pysam (<< 0.15~)
 Section: libs
 Priority: optional
 Multi-Arch: same
 Homepage: https://github.com/samtools/htslib
 Description: C library for high-throughput sequencing data formats
  HTSlib is an implementation of a unified C library for accessing common file
  formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
  Format), used for high-throughput sequencing data, and is the core library
  used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
  compatible with gcc, g++ and clang.
  .
  HTSlib implements a generalized BAM (binary SAM) index, with file extension
  ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
  new index and then for the old if the new index is absent.

drwxr-xr-x root/root         0 2020-08-03 11:19 ./
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root    734636 2020-08-03 11:19 ./usr/lib/arm-linux-gnueabihf/libhts.so.1.10.2-5
lrwxrwxrwx root/root         0 2020-08-03 11:19 ./usr/lib/arm-linux-gnueabihf/libhts.so.3 -> libhts.so.1.10.2-5
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/doc/libhts3/
-rw-r--r-- root/root      5339 2020-08-03 11:19 ./usr/share/doc/libhts3/changelog.Debian.gz
-rw-r--r-- root/root     15663 2019-12-19 09:52 ./usr/share/doc/libhts3/changelog.gz
-rw-r--r-- root/root      5817 2020-08-03 11:19 ./usr/share/doc/libhts3/copyright
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/man/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/man/man7/
-rw-r--r-- root/root      1886 2020-08-03 11:19 ./usr/share/man/man7/htslib-s3-plugin.7.gz


tabix-dbgsym_1.10.2-5_armhf.deb
-------------------------------

 new Debian package, version 2.0.
 size 1579556 bytes: control archive=700 bytes.
     448 bytes,    12 lines      control              
     403 bytes,     4 lines      md5sums              
 Package: tabix-dbgsym
 Source: htslib
 Version: 1.10.2-5
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1744
 Depends: tabix (= 1.10.2-5)
 Section: debug
 Priority: optional
 Description: debug symbols for tabix
 Build-Ids: 16c3baf77adf0c7d598684e024b9a389d471655b be3d87f407c881bd8dc5fa76a128c8a4f5ac4a74 c1b922c33a7f751f646b1b572100d151c9f31d37

drwxr-xr-x root/root         0 2020-08-03 11:19 ./
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/debug/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/debug/.build-id/16/
-rw-r--r-- root/root    738224 2020-08-03 11:19 ./usr/lib/debug/.build-id/16/c3baf77adf0c7d598684e024b9a389d471655b.debug
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/debug/.build-id/be/
-rw-r--r-- root/root    713632 2020-08-03 11:19 ./usr/lib/debug/.build-id/be/3d87f407c881bd8dc5fa76a128c8a4f5ac4a74.debug
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/debug/.build-id/c1/
-rw-r--r-- root/root    208872 2020-08-03 11:19 ./usr/lib/debug/.build-id/c1/b922c33a7f751f646b1b572100d151c9f31d37.debug
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root    109632 2020-08-03 11:19 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-08-03 11:19 ./usr/share/doc/tabix-dbgsym -> tabix


tabix_1.10.2-5_armhf.deb
------------------------

 new Debian package, version 2.0.
 size 319428 bytes: control archive=1132 bytes.
     967 bytes,    19 lines      control              
     545 bytes,     9 lines      md5sums              
 Package: tabix
 Source: htslib
 Version: 1.10.2-5
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1115
 Depends: libbz2-1.0, libc6 (>= 2.15), libcurl3-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0)
 Section: science
 Priority: optional
 Homepage: https://github.com/samtools/htslib
 Description: generic indexer for TAB-delimited genome position files
  Tabix indexes files where some columns indicate sequence coordinates: name
  (usually a chromosome), start and stop. The input data file must be position
  sorted and compressed by bgzip (provided in this package), which has a gzip
  like interface. After indexing, tabix is able to quickly retrieve data lines by
  chromosomal coordinates. Fast data retrieval also works over network if an URI
  is given as a file name.
  .
  This version of tabix is built from the HTSlib source.

drwxr-xr-x root/root         0 2020-08-03 11:19 ./
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/bin/
-rwxr-xr-x root/root    116328 2020-08-03 11:19 ./usr/bin/bgzip
-rwxr-xr-x root/root    480864 2020-08-03 11:19 ./usr/bin/htsfile
-rwxr-xr-x root/root    497240 2020-08-03 11:19 ./usr/bin/tabix
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/doc/tabix/
-rw-r--r-- root/root      5339 2020-08-03 11:19 ./usr/share/doc/tabix/changelog.Debian.gz
-rw-r--r-- root/root     15663 2019-12-19 09:52 ./usr/share/doc/tabix/changelog.gz
-rw-r--r-- root/root      5817 2020-08-03 11:19 ./usr/share/doc/tabix/copyright
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/man/
drwxr-xr-x root/root         0 2020-08-03 11:19 ./usr/share/man/man1/
-rw-r--r-- root/root      2604 2020-08-03 11:19 ./usr/share/man/man1/bgzip.1.gz
-rw-r--r-- root/root      1919 2020-08-03 11:19 ./usr/share/man/man1/htsfile.1.gz
-rw-r--r-- root/root      2831 2020-08-03 11:19 ./usr/share/man/man1/tabix.1.gz


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


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

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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

Build Architecture: armhf
Build-Space: 64144
Build-Time: 1616
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 395
Job: htslib_1.10.2-5
Machine Architecture: armhf
Package: htslib
Package-Time: 2062
Source-Version: 1.10.2-5
Space: 64144
Status: successful
Version: 1.10.2-5
--------------------------------------------------------------------------------
Finished at 2020-08-05T05:30:53Z
Build needed 00:34:22, 64144k disc space