samtools →
1.11-1 →
armhf → 2020-10-07 09:01:31
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| samtools 1.11-1 (armhf) Wed, 07 Oct 2020 08:52:04 +0000 |
+==============================================================================+
Package: samtools
Version: 1.11-1
Source Version: 1.11-1
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-91661ea9-56df-4162-b3d6-51898d58e639' 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 [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.4 MB in 9s (2679 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: 'samtools' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/samtools.git
Please use:
git clone https://salsa.debian.org/med-team/samtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 4539 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main samtools 1.11-1 (dsc) [2248 B]
Get:2 http://172.17.0.1/private bullseye-staging/main samtools 1.11-1 (tar) [4516 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main samtools 1.11-1 (diff) [20.1 kB]
Fetched 4539 kB in 1s (4909 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/samtools-Qdamon/samtools-1.11' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/samtools-Qdamon' 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-R99bNL/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-R99bNL/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-R99bNL/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-R99bNL/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-R99bNL/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-R99bNL/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-R99bNL/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-R99bNL/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (9634 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 37 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-R99bNL/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (65.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12498 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), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.11), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0), liblzma-dev, libbz2-dev
Filtered Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.11), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0), liblzma-dev, libbz2-dev
dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/<<BUILDDIR>>/resolver-R99bNL/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-samtools-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-R99bNL/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-R99bNL/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-R99bNL/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-R99bNL/apt_archive ./ Sources [592 B]
Get:5 copy:/<<BUILDDIR>>/resolver-R99bNL/apt_archive ./ Packages [664 B]
Fetched 2589 B in 0s (11.8 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install samtools 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 autoconf-archive automake autopoint autotools-dev bash-completion
debhelper dh-autoreconf 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 libhts-dev libhts3 libicu67 libio-pty-perl
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc
libmagic1 libncurses-dev libncurses5-dev libncurses6 libncursesw6
libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl1.1
libsub-override-perl libtinfo6 libtool libuchardet0 libxml2 m4 man-db
pkg-config po-debconf tabix zlib1g-dev
Suggested packages:
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 krb5-doc krb5-user liblzma-doc
ncurses-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 libgpm2
publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bash-completion
debhelper dh-autoreconf 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 libhts-dev libhts3 libicu67 libio-pty-perl
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc
libmagic1 libncurses-dev libncurses5-dev libncurses6 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl1.1
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config
po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
The following packages will be upgraded:
libncursesw6 libtinfo6
2 upgraded, 60 newly installed, 0 to remove and 35 not upgraded.
Need to get 27.8 MB/29.0 MB of archives.
After this operation, 94.8 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-R99bNL/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [948 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 1.5.3-1 [29.9 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 autoconf-archive all 20190106-2.1 [746 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.2+20200918-1 [327 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.2+20200918-1 [105 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf bash-completion all 1:2.11-2 [234 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.181-1 [161 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.0-2 [1173 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6 [578 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2 [259 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-10+b3 [62.0 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-10+b3 [112 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-10+b3 [318 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-10+b3 [135 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.41.0-3 [63.0 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.72.0-1 [297 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.72.0-1 [371 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.6-1 [40.8 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-2 [318 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-2 [4495 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libio-pty-perl armhf 1:1.12-1 [35.5 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20200918-1 [79.5 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.2+20200918-1 [290 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.2+20200918-1 [940 B]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf tabix armhf 1.11-2 [283 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libtinfo6:armhf (6.2+20200918-1) ...
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Selecting previously unselected package gettext.
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Unpacking intltool-debian (0.35.0+20060710.5) ...
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Unpacking po-debconf (1.0.21) ...
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Unpacking debhelper (13.2.1) ...
Selecting previously unselected package libbrotli1:armhf.
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Unpacking libbrotli1:armhf (1.0.9-2) ...
Selecting previously unselected package libbz2-dev:armhf.
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Unpacking libbz2-dev:armhf (1.0.8-4) ...
Selecting previously unselected package libkrb5support0:armhf.
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Unpacking libkrb5support0:armhf (1.17-10+b3) ...
Selecting previously unselected package libk5crypto3:armhf.
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Unpacking libk5crypto3:armhf (1.17-10+b3) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../32-libkeyutils1_1.6.1-2_armhf.deb ...
Unpacking libkeyutils1:armhf (1.6.1-2) ...
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Unpacking libssl1.1:armhf (1.1.1g-1) ...
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Unpacking libkrb5-3:armhf (1.17-10+b3) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
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Unpacking libgssapi-krb5-2:armhf (1.17-10+b3) ...
Selecting previously unselected package libnghttp2-14:armhf.
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Unpacking libnghttp2-14:armhf (1.41.0-3) ...
Selecting previously unselected package libpsl5:armhf.
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Unpacking libpsl5:armhf (0.21.0-1.1) ...
Selecting previously unselected package librtmp1:armhf.
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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
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Unpacking libdeflate0:armhf (1.6-1) ...
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Unpacking libhts3:armhf (1.11-2) ...
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Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
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Unpacking libhts-dev:armhf (1.11-2) ...
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Unpacking libio-pty-perl (1:1.12-1) ...
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Unpacking pkg-config (0.29.2-1) ...
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Unpacking tabix (1.11-2) ...
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Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.21.0-1.1) ...
Setting up libicu67:armhf (67.1-4) ...
Setting up libio-pty-perl (1:1.12-1) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.0-2) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1g-1) ...
Setting up libdebhelper-perl (13.2.1) ...
Setting up libbrotli1:armhf (1.0.9-2) ...
Setting up libnghttp2-14:armhf (1.41.0-3) ...
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 autoconf-archive (20190106-2.1) ...
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 bash-completion (1:2.11-2) ...
Setting up libncurses6:armhf (6.2+20200918-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up pkg-config (0.29.2-1) ...
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 tabix (1.11-2) ...
Setting up libelf1:armhf (0.181-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6) ...
Setting up libbz2-dev:armhf (1.0.8-4) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libncurses-dev:armhf (6.2+20200918-1) ...
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 libncurses5-dev:armhf (6.2+20200918-1) ...
Setting up automake (1:1.16.2-4) ...
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 (7.72.0-1) ...
Setting up libcurl4-gnutls-dev:armhf (7.72.0-1) ...
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 libhts3:armhf (1.11-2) ...
Setting up po-debconf (1.0.21) ...
Setting up libhts-dev:armhf (1.11-2) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2.1) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-5+rpi1 gcc-10_10.2.0-5+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 autoconf-archive_20190106-2.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-7 bash-completion_1:2.11-2 binutils_2.35-2+rpi1 binutils-arm-linux-gnueabihf_2.35-2+rpi1 binutils-common_2.35-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.30-3 cpp_4:10.1.0-1+rpi1 cpp-10_10.2.0-5+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.1.0-1+rpi1 g++-10_10.2.0-5+rpi1 gcc_4:10.1.0-1+rpi1 gcc-10_10.2.0-5+rpi1 gcc-10-base_10.2.0-5+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_3:20200821-2 libacl1_2.2.53-8 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-5+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-5+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.35-2+rpi1 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-6+b1 libbrotli1_1.0.9-2 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-3+rpi1 libc-dev-bin_2.31-3+rpi1 libc6_2.31-3+rpi1 libc6-dev_2.31-3+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.43-1 libcap2-bin_1:2.43-1 libcc1-0_10.2.0-5+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35-2+rpi1 libctf0_2.35-2+rpi1 libcurl3-gnutls_7.72.0-1 libcurl4-gnutls-dev_7.72.0-1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2.1 libdeflate-dev_1.6-1 libdeflate0_1.6-1 libdpkg-perl_1.20.5+rpi1 libelf1_0.181-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-5+rpi1 libgcc-s1_10.2.0-5+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.0-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.2.0-5+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libhogweed6_3.6-2 libhts-dev_1.11-2 libhts3_1.11-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libio-pty-perl_1:1.12-1 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_2.4.51+dfsg-1 libldap-common_2.4.51+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_2.36-3 libmpc3_1.2.0~rc1-1 libmpfr6_4.1.0-3 libncurses-dev_6.2+20200918-1 libncurses5-dev_6.2+20200918-1 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 libnpth0_1.6-2 libp11-kit0_0.23.21-2 libpam-cap_1:2.43-1 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_1.5.3-1 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_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.2-1+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtool_2.4.6-14 libubsan1_10.2.0-5+rpi1 libuchardet0_0.0.7-1 libudev1_246.2-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3 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 pkg-config_0.29.2-1 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-samtools-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-4 tabix_1.11-2 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-3 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 '/tmp/dpkg-verify-sig.4en7qZTG/trustedkeys.kbx': General error
gpgv: Signature made Thu Oct 1 14:52:01 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 ./samtools_1.11-1.dsc
dpkg-source: info: extracting samtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking samtools_1.11.orig.tar.gz
dpkg-source: info: unpacking samtools_1.11-1.debian.tar.xz
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-91661ea9-56df-4162-b3d6-51898d58e639
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package samtools
dpkg-buildpackage: info: source version 1.11-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from samtools-1.11/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f config.mk
touch config.mk
dh_auto_clean --
install -d /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home
make -j4 distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd test/dat && rm -f test_input_*.bam.bai
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o
rm -f samtools libbam.a libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
rm -rf autom4te.cache
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files
rm -fr -- debian/samtools/ debian/tmp/ debian/samtools-test/
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
configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
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>>'
touch config.mk
aclocal --force -I debian/ -I /usr/share/aclocal
configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
autoconf
configure.ac:64: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
dh_auto_configure -- --with-htslib=system
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 --with-htslib=system
checking for gawk... no
checking for mawk... mawk
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 grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for Curses library... yes
checking for working curses.h... yes
checking for X/Open Enhanced Curses conformance... no
checking for Curses color functions... yes
checking for obsolete Curses functions... yes
checking for library containing cbreak... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/samtools.debhelper.log
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
make -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
echo '#define SAMTOOLS_VERSION "1.11"' > version.h
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -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 -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -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 -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
ar -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz
gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o ./lz4/lz4.o libbam.a libst.a -lhts -lcurses -lm -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/samtools.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -- BGZIP=/usr/bin/bgzip
make -j4 test VERBOSE=1 BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/<<PKGBUILDDIR>>'
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
test/split/test_parse_args
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-}
/usr/bin/bgzip -c -b 65272 -s 5 /tmp/ziD2sgGUfK/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 979200 -s 6 /tmp/ziD2sgGUfK/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 652804 -s 6 /tmp/ziD2sgGUfK/bgzip.dat.gz
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/ziD2sgGUfK/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/ziD2sgGUfK/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/ziD2sgGUfK/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/ziD2sgGUfK/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/ziD2sgGUfK/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/ziD2sgGUfK/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/ziD2sgGUfK/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/ziD2sgGUfK/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/ziD2sgGUfK/fqidx.fq 3:11-13
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/ziD2sgGUfK/fqidx.fq.gz 3:11-13
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/ziD2sgGUfK/fqidx.fq 2:998-1003
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/ziD2sgGUfK/fqidx.fq.gz 2:998-1003
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/ziD2sgGUfK/fqidx.fq 1:100-104
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/ziD2sgGUfK/fqidx.fq.gz 1:100-104
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/ziD2sgGUfK/fqidx.fq 1:99998-100007
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/ziD2sgGUfK/fqidx.fq.gz 1:99998-100007
.. ok
.. ok
test_dict:
/<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /<<PKGBUILDDIR>>/test/dat/dict.fa
.. ok
test_dict:
/<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/ziD2sgGUfK/dict.fa.gz
.. ok
test_dict:
cat /<<PKGBUILDDIR>>/test/dat/dict.fa | /<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz
.. ok
test_dict:
/<<PKGBUILDDIR>>/samtools dict -AH < /<<PKGBUILDDIR>>/test/dat/dict.alias.fa
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view /tmp/ziD2sgGUfK/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view /tmp/ziD2sgGUfK/large_chrom.bam ref2:1-541556283
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam && cat /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/ziD2sgGUfK/test_input_1_b.bam.bai ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools merge -O sam - -X -cp -R ref2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai /tmp/ziD2sgGUfK/test_input_1_b.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam /tmp/ziD2sgGUfK/auto_indexed.csi && cat /tmp/ziD2sgGUfK/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.cram /tmp/ziD2sgGUfK/auto_indexed.crai && cat /tmp/ziD2sgGUfK/auto_indexed.crai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.sam /tmp/ziD2sgGUfK/auto_indexed.csi && cat /tmp/ziD2sgGUfK/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/ziD2sgGUfK/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/ziD2sgGUfK/large_chrom.bam ref2:1-541556283
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam && cat /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/ziD2sgGUfK/test_input_1_b.bam.bai ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -O sam - -X -cp -R ref2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai /tmp/ziD2sgGUfK/test_input_1_b.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam /tmp/ziD2sgGUfK/auto_indexed.csi && cat /tmp/ziD2sgGUfK/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.cram /tmp/ziD2sgGUfK/auto_indexed.crai && cat /tmp/ziD2sgGUfK/auto_indexed.crai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.sam /tmp/ziD2sgGUfK/auto_indexed.csi && cat /tmp/ziD2sgGUfK/auto_indexed.csi
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/ziD2sgGUfK/mpileup.bam.list -f /tmp/ziD2sgGUfK/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/ziD2sgGUfK/mpileup.cram.list -f /tmp/ziD2sgGUfK/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/ziD2sgGUfK/mpileup.bam.urllist -f /tmp/ziD2sgGUfK/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/ziD2sgGUfK/mpileup.cram.urllist -f /tmp/ziD2sgGUfK/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/ziD2sgGUfK/mpileup.bam.list -f /tmp/ziD2sgGUfK/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/ziD2sgGUfK/mpileup.cram.list -f /tmp/ziD2sgGUfK/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/ziD2sgGUfK/mpileup.cram.list -f /tmp/ziD2sgGUfK/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/ziD2sgGUfK/mpileup.cram.list -f /tmp/ziD2sgGUfK/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/ziD2sgGUfK/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ziD2sgGUfK/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/ziD2sgGUfK/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ziD2sgGUfK/mpileup.1.cram | grep -v mpileup
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup /<<PKGBUILDDIR>>/test/mpileup/overlap.bam | grep 128814202
.. ok
test_usage:
samtools
samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, tview, view, depad
.. ok
test_usage_subcommand:
samtools dict
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools faidx
.. ok
test_usage_subcommand:
samtools fqidx
.. ok
test_usage_subcommand:
samtools index
.. ok
test_usage_subcommand:
samtools calmd
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools fixmate
.. ok
test_usage_subcommand:
samtools reheader
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools targetcut
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools addreplacerg
.. ok
test_usage_subcommand:
samtools markdup
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools ampliconclip
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools collate
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools cat
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools merge
.. ok
test_usage_subcommand:
samtools mpileup
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools sort
.. ok
test_usage_subcommand:
samtools split
.. ok
test_usage_subcommand:
samtools quickcheck
.. ok
test_usage_subcommand:
samtools fastq
.. ok
test_usage_subcommand:
samtools fasta
.. ok
test_usage_subcommand:
samtools bedcov
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools coverage
.. ok
test_usage_subcommand:
samtools depth
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools flagstat
.. ok
test_usage_subcommand:
samtools idxstats
.. ok
test_usage_subcommand:
samtools phase
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools stats
.. ok
test_usage_subcommand:
samtools ampliconstats
.. ok
test_usage_subcommand:
samtools flags
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools tview
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools view
.. ok
test_usage_subcommand:
samtools depad
Usage on stderr rather than stdout
.. expected failure
test_view:
Generating test data file .................. done
1: SAM -> BAM -> SAM .. ok
2: SAM -> uncompressed BAM .. ok
3: uncompressed BAM -> SAM and compare .. ok
4: SAM -> fast compressed BAM .. ok
5: fast compressed BAM -> SAM and compare .. ok
6: SAM -> CRAM -> SAM (UR header tags) .. ok
7: SAM -> CRAM -> SAM (M5 header tags) .. ok
8: BAM -> CRAM with UR -> SAM .. ok
9: SAM -> BAM (M5 header tags) .. ok
10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok
11: CRAM -> BAM with UR .. ok
12: CRAM -> BAM with M5 .. ok
13: SAM -> SAM via stdout .. ok
14: SAM -> BAM via stdout .. ok
15: SAM -> CRAM via stdout .. ok
16: SAM from stdin -> SAM .. ok
17: BAM from stdin -> SAM .. ok
18: CRAM from stdin -> SAM .. ok
19: samtools view -H (SAM input) .. ok
20: samtools view -H (BAM input) .. ok
21: samtools view -H (CRAM input) .. ok
22: No headers (SAM input) .. ok
23: No headers (BAM input) .. ok
24: No headers (CRAM input) .. ok
25: Filter -f 128 (SAM input) .. ok
26: Count -f 128 (SAM input) .. ok
27: Filter -f 128 (BAM input) .. ok
28: Count -f 128 (BAM input) .. ok
29: Filter -f 128 (CRAM input) .. ok
30: Count -f 128 (CRAM input) .. ok
31: Filter -F 128 (SAM input) .. ok
32: Count -F 128 (SAM input) .. ok
33: Filter -F 128 (BAM input) .. ok
34: Count -F 128 (BAM input) .. ok
35: Filter -F 128 (CRAM input) .. ok
36: Count -F 128 (CRAM input) .. ok
37: Filter -F 128 -f 2 (SAM input) .. ok
38: Count -F 128 -f 2 (SAM input) .. ok
39: Filter -F 128 -f 2 (BAM input) .. ok
40: Count -F 128 -f 2 (BAM input) .. ok
41: Filter -F 128 -f 2 (CRAM input) .. ok
42: Count -F 128 -f 2 (CRAM input) .. ok
43: Filter -r grp2 (SAM input) .. ok
44: Count -r grp2 (SAM input) .. ok
45: Filter -r grp2 (BAM input) .. ok
46: Count -r grp2 (BAM input) .. ok
47: Filter -r grp2 (CRAM input) .. ok
48: Count -r grp2 (CRAM input) .. ok
49: Filter -R /tmp/ziD2sgGUfK/view.001.fogn (SAM input) .. ok
50: Count -R /tmp/ziD2sgGUfK/view.001.fogn (SAM input) .. ok
51: Filter -R /tmp/ziD2sgGUfK/view.001.fogn (BAM input) .. ok
52: Count -R /tmp/ziD2sgGUfK/view.001.fogn (BAM input) .. ok
53: Filter -R /tmp/ziD2sgGUfK/view.001.fogn (CRAM input) .. ok
54: Count -R /tmp/ziD2sgGUfK/view.001.fogn (CRAM input) .. ok
55: Filter -R /tmp/ziD2sgGUfK/view.001.fogn -r grp2 (SAM input).. ok
56: Count -R /tmp/ziD2sgGUfK/view.001.fogn -r grp2 (SAM input).. ok
57: Filter -R /tmp/ziD2sgGUfK/view.001.fogn -r grp2 (BAM input).. ok
58: Count -R /tmp/ziD2sgGUfK/view.001.fogn -r grp2 (BAM input).. ok
59: Filter -R /tmp/ziD2sgGUfK/view.001.fogn -r grp2 (CRAM input).. ok
60: Count -R /tmp/ziD2sgGUfK/view.001.fogn -r grp2 (CRAM input).. ok
61: Filter -r grp2 -R /tmp/ziD2sgGUfK/view.001.fogn (SAM input).. ok
62: Count -r grp2 -R /tmp/ziD2sgGUfK/view.001.fogn (SAM input).. ok
63: Filter -r grp2 -R /tmp/ziD2sgGUfK/view.001.fogn (BAM input).. ok
64: Count -r grp2 -R /tmp/ziD2sgGUfK/view.001.fogn (BAM input).. ok
65: Filter -r grp2 -R /tmp/ziD2sgGUfK/view.001.fogn (CRAM input).. ok
66: Count -r grp2 -R /tmp/ziD2sgGUfK/view.001.fogn (CRAM input).. ok
67: Filter -d BC:TGCA (SAM input) .. ok
68: Count -d BC:TGCA (SAM input) .. ok
69: Filter -d BC:TGCA (BAM input) .. ok
70: Count -d BC:TGCA (BAM input) .. ok
71: Filter -d BC:TGCA (CRAM input) .. ok
72: Count -d BC:TGCA (CRAM input) .. ok
73: Filter -D BC:/tmp/ziD2sgGUfK/view.001.fobc (SAM input) .. ok
74: Count -D BC:/tmp/ziD2sgGUfK/view.001.fobc (SAM input) .. ok
75: Filter -D BC:/tmp/ziD2sgGUfK/view.001.fobc (BAM input) .. ok
76: Count -D BC:/tmp/ziD2sgGUfK/view.001.fobc (BAM input) .. ok
77: Filter -D BC:/tmp/ziD2sgGUfK/view.001.fobc (CRAM input) .. ok
78: Count -D BC:/tmp/ziD2sgGUfK/view.001.fobc (CRAM input) .. ok
79: Filter -D BC:/tmp/ziD2sgGUfK/view.001.fobc -d BC:TGCA (SAM input).. ok
80: Count -D BC:/tmp/ziD2sgGUfK/view.001.fobc -d BC:TGCA (SAM input).. ok
81: Filter -D BC:/tmp/ziD2sgGUfK/view.001.fobc -d BC:TGCA (BAM input).. ok
82: Count -D BC:/tmp/ziD2sgGUfK/view.001.fobc -d BC:TGCA (BAM input).. ok
83: Filter -D BC:/tmp/ziD2sgGUfK/view.001.fobc -d BC:TGCA (CRAM input).. ok
84: Count -D BC:/tmp/ziD2sgGUfK/view.001.fobc -d BC:TGCA (CRAM input).. ok
85: Filter -d BC:TGCA -D BC:/tmp/ziD2sgGUfK/view.001.fobc (SAM input).. ok
86: Count -d BC:TGCA -D BC:/tmp/ziD2sgGUfK/view.001.fobc (SAM input).. ok
87: Filter -d BC:TGCA -D BC:/tmp/ziD2sgGUfK/view.001.fobc (BAM input).. ok
88: Count -d BC:TGCA -D BC:/tmp/ziD2sgGUfK/view.001.fobc (BAM input).. ok
89: Filter -d BC:TGCA -D BC:/tmp/ziD2sgGUfK/view.001.fobc (CRAM input).. ok
90: Count -d BC:TGCA -D BC:/tmp/ziD2sgGUfK/view.001.fobc (CRAM input).. ok
91: Filter -D RG:/tmp/ziD2sgGUfK/view.001.fogn (SAM input) .. ok
92: Count -D RG:/tmp/ziD2sgGUfK/view.001.fogn (SAM input) .. ok
93: Filter -D RG:/tmp/ziD2sgGUfK/view.001.fogn (BAM input) .. ok
94: Count -D RG:/tmp/ziD2sgGUfK/view.001.fogn (BAM input) .. ok
95: Filter -D RG:/tmp/ziD2sgGUfK/view.001.fogn (CRAM input) .. ok
96: Count -D RG:/tmp/ziD2sgGUfK/view.001.fogn (CRAM input) .. ok
97: Filter -d NE:TGCA (SAM input) .. ok
98: Count -d NE:TGCA (SAM input) .. ok
99: Filter -d NE:TGCA (BAM input) .. ok
100: Count -d NE:TGCA (BAM input) .. ok
101: Filter -d NE:TGCA (CRAM input) .. ok
102: Count -d NE:TGCA (CRAM input) .. ok
103: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/ziD2sgGUfK/view.test103.sam -h -d TGCA /tmp/ziD2sgGUfK/view.001.sam --no-PG
.. expected failure
104: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d TGCA /tmp/ziD2sgGUfK/view.001.sam --no-PG
.. expected failure
105: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/ziD2sgGUfK/view.test105.sam -h -d TGCA /tmp/ziD2sgGUfK/view.test001.bam --no-PG
.. expected failure
106: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d TGCA /tmp/ziD2sgGUfK/view.test001.bam --no-PG
.. expected failure
107: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/ziD2sgGUfK/view.test107.sam -h -d TGCA /tmp/ziD2sgGUfK/view.test006.cram --no-PG
.. expected failure
108: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d TGCA /tmp/ziD2sgGUfK/view.test006.cram --no-PG
.. expected failure
109: Filter -D BClong:/tmp/ziD2sgGUfK/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ziD2sgGUfK/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/ziD2sgGUfK/view.test109.sam -h -D BClong:/tmp/ziD2sgGUfK/view.001.fobc /tmp/ziD2sgGUfK/view.001.sam --no-PG
.. expected failure
110: Count -D BClong:/tmp/ziD2sgGUfK/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ziD2sgGUfK/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/ziD2sgGUfK/view.001.fobc /tmp/ziD2sgGUfK/view.001.sam --no-PG
.. expected failure
111: Filter -D BClong:/tmp/ziD2sgGUfK/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ziD2sgGUfK/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/ziD2sgGUfK/view.test111.sam -h -D BClong:/tmp/ziD2sgGUfK/view.001.fobc /tmp/ziD2sgGUfK/view.test001.bam --no-PG
.. expected failure
112: Count -D BClong:/tmp/ziD2sgGUfK/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ziD2sgGUfK/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/ziD2sgGUfK/view.001.fobc /tmp/ziD2sgGUfK/view.test001.bam --no-PG
.. expected failure
113: Filter -D BClong:/tmp/ziD2sgGUfK/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ziD2sgGUfK/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/ziD2sgGUfK/view.test113.sam -h -D BClong:/tmp/ziD2sgGUfK/view.001.fobc /tmp/ziD2sgGUfK/view.test006.cram --no-PG
.. expected failure
114: Count -D BClong:/tmp/ziD2sgGUfK/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ziD2sgGUfK/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/ziD2sgGUfK/view.001.fobc /tmp/ziD2sgGUfK/view.test006.cram --no-PG
.. expected failure
115: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/ziD2sgGUfK/view.test115.sam -h -d BC:ACGT -d RG:grp2 /tmp/ziD2sgGUfK/view.001.sam --no-PG
.. expected failure
116: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/ziD2sgGUfK/view.001.sam --no-PG
.. expected failure
117: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/ziD2sgGUfK/view.test117.sam -h -d BC:ACGT -d RG:grp2 /tmp/ziD2sgGUfK/view.test001.bam --no-PG
.. expected failure
118: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/ziD2sgGUfK/view.test001.bam --no-PG
.. expected failure
119: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/ziD2sgGUfK/view.test119.sam -h -d BC:ACGT -d RG:grp2 /tmp/ziD2sgGUfK/view.test006.cram --no-PG
.. expected failure
120: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/ziD2sgGUfK/view.test006.cram --no-PG
.. expected failure
121: Filter -l Library 2 (SAM input) .. ok
122: Count -l Library 2 (SAM input) .. ok
123: Filter -l Library 2 (BAM input) .. ok
124: Count -l Library 2 (BAM input) .. ok
125: Filter -l Library 2 (CRAM input) .. ok
126: Count -l Library 2 (CRAM input) .. ok
127: Filter -l Library 3 (SAM input) .. ok
128: Count -l Library 3 (SAM input) .. ok
129: Filter -l Library 3 (BAM input) .. ok
130: Count -l Library 3 (BAM input) .. ok
131: Filter -l Library 3 (CRAM input) .. ok
132: Count -l Library 3 (CRAM input) .. ok
133: Filter -q 50 (SAM input) .. ok
134: Count -q 50 (SAM input) .. ok
135: Filter -q 50 (BAM input) .. ok
136: Count -q 50 (BAM input) .. ok
137: Filter -q 50 (CRAM input) .. ok
138: Count -q 50 (CRAM input) .. ok
139: Filter -q 99 (SAM input) .. ok
140: Count -q 99 (SAM input) .. ok
141: Filter -q 99 (BAM input) .. ok
142: Count -q 99 (BAM input) .. ok
143: Filter -q 99 (CRAM input) .. ok
144: Count -q 99 (CRAM input) .. ok
145: Filter -q 100 (SAM input) .. ok
146: Count -q 100 (SAM input) .. ok
147: Filter -q 100 (BAM input) .. ok
148: Count -q 100 (BAM input) .. ok
149: Filter -q 100 (CRAM input) .. ok
150: Count -q 100 (CRAM input) .. ok
151: Filter -x fa (SAM input) .. ok
152: Count -x fa (SAM input) .. ok
153: Filter -x fa (BAM input) .. ok
154: Count -x fa (BAM input) .. ok
155: Filter -x fa (CRAM input) .. ok
156: Count -x fa (CRAM input) .. ok
157: Filter -x fa -x ha (SAM input) .. ok
158: Count -x fa -x ha (SAM input) .. ok
159: Filter -x fa -x ha (BAM input) .. ok
160: Count -x fa -x ha (BAM input) .. ok
161: Filter -x fa -x ha (CRAM input) .. ok
162: Count -x fa -x ha (CRAM input) .. ok
163: Filter -x fa -r grp2 (SAM input) .. ok
164: Count -x fa -r grp2 (SAM input) .. ok
165: Filter -x fa -r grp2 (BAM input) .. ok
166: Count -x fa -r grp2 (BAM input) .. ok
167: Filter -x fa -r grp2 (CRAM input) .. ok
168: Count -x fa -r grp2 (CRAM input) .. ok
169: Filter -x RG -r grp2 (SAM input) .. ok
170: Count -x RG -r grp2 (SAM input) .. ok
171: Filter -x RG -r grp2 (BAM input) .. ok
172: Count -x RG -r grp2 (BAM input) .. ok
173: Filter -x RG -r grp2 (CRAM input) .. ok
174: Count -x RG -r grp2 (CRAM input) .. ok
175: Filter -m 10 (SAM input) .. ok
176: Count -m 10 (SAM input) .. ok
177: Filter -m 10 (BAM input) .. ok
178: Count -m 10 (BAM input) .. ok
179: Filter -m 10 (CRAM input) .. ok
180: Count -m 10 (CRAM input) .. ok
181: Filter -m 11 (SAM input) .. ok
182: Count -m 11 (SAM input) .. ok
183: Filter -m 11 (BAM input) .. ok
184: Count -m 11 (BAM input) .. ok
185: Filter -m 11 (CRAM input) .. ok
186: Count -m 11 (CRAM input) .. ok
187: Filter -m 15 (SAM input) .. ok
188: Count -m 15 (SAM input) .. ok
189: Filter -m 15 (BAM input) .. ok
190: Count -m 15 (BAM input) .. ok
191: Filter -m 15 (CRAM input) .. ok
192: Count -m 15 (CRAM input) .. ok
193: Filter -m 16 (SAM input) .. ok
194: Count -m 16 (SAM input) .. ok
195: Filter -m 16 (BAM input) .. ok
196: Count -m 16 (BAM input) .. ok
197: Filter -m 16 (CRAM input) .. ok
198: Count -m 16 (CRAM input) .. ok
199: 1bp reads file SAM -> BAM -> SAM .. ok
200: 1bp reads file SAM -> CRAM -> SAM .. ok
200: Region Z (BAM input) .. ok
201: Count Z (BAM input) .. ok
202: Region Z (CRAM input) .. ok
203: Count Z (CRAM input) .. ok
204: Region Z:30 (BAM input) .. ok
205: Count Z:30 (BAM input) .. ok
206: Region Z:30 (CRAM input) .. ok
207: Count Z:30 (CRAM input) .. ok
208: Region Z:20-40 (BAM input) .. ok
209: Count Z:20-40 (BAM input) .. ok
210: Region Z:20-40 (CRAM input) .. ok
211: Count Z:20-40 (CRAM input) .. ok
212: Region ref1 (BAM input) .. ok
213: Count ref1 (BAM input) .. ok
214: Region ref1 (CRAM input) .. ok
215: Count ref1 (CRAM input) .. ok
216: Region ref1:15 (BAM input) .. ok
217: Count ref1:15 (BAM input) .. ok
218: Region ref1:15 (CRAM input) .. ok
219: Count ref1:15 (CRAM input) .. ok
220: Region ref1:15-45 (BAM input) .. ok
221: Count ref1:15-45 (BAM input) .. ok
222: Region ref1:15-45 (CRAM input) .. ok
223: Count ref1:15-45 (CRAM input) .. ok
224: Region ref1:15-45 ref2 (BAM input) .. ok
225: Count ref1:15-45 ref2 (BAM input) .. ok
226: Region ref1:15-45 ref2 (CRAM input) .. ok
227: Count ref1:15-45 ref2 (CRAM input) .. ok
228: Region ref1:15-45 ref2:16 (BAM input) .. ok
229: Count ref1:15-45 ref2:16 (BAM input) .. ok
230: Region ref1:15-45 ref2:16 (CRAM input) .. ok
231: Count ref1:15-45 ref2:16 (CRAM input) .. ok
232: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
233: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
234: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
235: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
236: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
237: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
238: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
239: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
240: Region -f 128 ref1 (BAM input) .. ok
241: Count -f 128 ref1 (BAM input) .. ok
242: Region -f 128 ref1 (CRAM input) .. ok
243: Count -f 128 ref1 (CRAM input) .. ok
244: Region -q 50 ref1:15-45 (BAM input) .. ok
245: Count -q 50 ref1:15-45 (BAM input) .. ok
246: Region -q 50 ref1:15-45 (CRAM input) .. ok
247: Count -q 50 ref1:15-45 (CRAM input) .. ok
248: Region -r grp2 ref1:15-45 (BAM input) .. ok
249: Count -r grp2 ref1:15-45 (BAM input) .. ok
250: Region -r grp2 ref1:15-45 (CRAM input) .. ok
251: Count -r grp2 ref1:15-45 (CRAM input) .. ok
252: Region * (BAM input) .. ok
253: Count * (BAM input) .. ok
254: Region * (CRAM input) .. ok
255: Count * (CRAM input) .. ok
256: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
257: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
258: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
259: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
260: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
261: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
262: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
263: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
264: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
265: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
266: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
267: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
268: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
269: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
270: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
271: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
272: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
273: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
274: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
275: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
276: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
277: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
278: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
279: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
280: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
281: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
282: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
283: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
284: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
285: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
286: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
287: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
288: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
289: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
290: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
291: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
292: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
293: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
294: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
295: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
296: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
297: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
298: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
299: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
300: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
301: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
302: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
303: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
304: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
305: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
306: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
307: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
308: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
309: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
310: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
311: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
312: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
313: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
314: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
315: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
316: Make BAM with no M5/UR tags .. ok
317: Add @SQ with -t (SAM -> SAM) .. ok
318: Add @SQ with -T (SAM -> SAM) .. ok
319: Add @SQ with -t (BAM -> SAM) .. ok
320: Add @SQ with -T (BAM -> SAM) .. ok
321: Add @SQ with -t (SAM -> BAM) .. ok
322: Add @SQ with -T (SAM -> BAM) .. ok
323: Add @SQ with -t (BAM -> BAM) .. ok
324: Add @SQ with -T (BAM -> BAM) .. ok
325: Add @SQ with -t (SAM -> CRAM) .. ok
326: Add @SQ with -T (SAM -> CRAM) .. ok
327: Add @SQ with -t (BAM -> CRAM) .. ok
328: Add @SQ with -T (BAM -> CRAM) .. ok
329: Make CRAM with no UR field .. ok
330: Decoding CRAM with no UR field via -T .. ok
331: CIGAR B-operator removal .. ok
332: Big SAM -> BAM .. ok
333: Big SAM -> BAM (2 threads) .. ok
334: Big SAM -> BAM (4 threads) .. ok
335: Big SAM -> CRAM .. ok
336: Big SAM -> CRAM (2 threads) .. ok
337: Big SAM -> CRAM (4 threads) .. ok
338: Subsample 0.2 (SAM input) ............ ok
339: Subsample 0.5 (SAM input) ............ ok
340: Subsample 0.8 (SAM input) ............ ok
341: Subsample 0.2 (BAM input) ............ ok
342: Subsample 0.5 (BAM input) ............ ok
343: Subsample 0.8 (BAM input) ............ ok
344: Subsample 0.2 (CRAM input) ............ ok
345: Subsample 0.5 (CRAM input) ............ ok
346: Subsample 0.8 (CRAM input) ............ ok
347: SAM add PG .. ok
test_cat:
Generating test data file .................. done
Generate BAM file #1 .. ok
Generate CRAM file #1 .. ok
Generating test data file .................. done
Generate BAM file #2 .. ok
Generate CRAM file #2 .. ok
Generating test data file .................. done
Generate BAM file #3 .. ok
Generate CRAM file #3 .. ok
Generating test data file .................. done
Generate BAM file #4 .. ok
Generate CRAM file #4 .. ok
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
3: cat CRAM files .. ok
4: cat BAM files to stdout .. ok
5: cat recompressed BAM files to stdout .. ok
6: cat CRAM files to stdout .. ok
7: cat BAM files with new header .. ok
8: cat recompressed BAM files with new header .. ok
9: cat CRAM files with new header .. ok
test_bam2fq:
Generate BAM file .. ok
Generate CRAM file .. ok
1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.002.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.003.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.010.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /<<PKGBUILDDIR>>/test/bc_split.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -t -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -t -T MD,ia -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -i --index-format 'i*i*' -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.703.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -1 /<<PKGBUILDDIR>>/test/o.fq -2 /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -o /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -s /tmp/ziD2sgGUfK/bam2fq.discard.s.fq -0 /tmp/ziD2sgGUfK/bam2fq.discard.0.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -T ba,bb,bc,bd,be,bf,bg /<<PKGBUILDDIR>>/test/dat/bam2fq.013.sam
.. ok
test_bam2fq:
Generate BAM file (2 threads) .. ok
Generate CRAM file (2 threads) .. ok
1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.002.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.003.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.010.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /<<PKGBUILDDIR>>/test/bc_split.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -t -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -t -T MD,ia -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -i --index-format 'i*i*' -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.703.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -1 /<<PKGBUILDDIR>>/test/o.fq -2 /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -o /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -s /tmp/ziD2sgGUfK/bam2fq.discard.s.fq -0 /tmp/ziD2sgGUfK/bam2fq.discard.0.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /<<PKGBUILDDIR>>/test/dat/bam2fq.013.sam
.. ok
test_depad:
Generate BAM file .. ok
depad (SAM input) .. ok
depad -s (SAM input) .. ok
depad -u (SAM input) .. ok
depad -1 (SAM input) .. ok
depad (BAM input) .. ok
depad -s (BAM input) .. ok
depad -u (BAM input) .. ok
depad -1 (BAM input) .. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/1_map_cigar_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/4_X_cigar_full_seq.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/5_insert_cigar_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa -i 0 /<<PKGBUILDDIR>>/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/7_supp_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/8_secondary_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -S RG -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -S RG -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -t /<<PKGBUILDDIR>>/test/stat/11.stats.targets /<<PKGBUILDDIR>>/test/stat/11_target.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -g 4 -t /<<PKGBUILDDIR>>/test/stat/11.stats.targets /<<PKGBUILDDIR>>/test/stat/11_target.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -g 4 /<<PKGBUILDDIR>>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -t /<<PKGBUILDDIR>>/test/stat/12_3reads.bed | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -p -t /<<PKGBUILDDIR>>/test/stat/12_3reads.bed | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -t /<<PKGBUILDDIR>>/test/stat/12_2reads.bed | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -p -t /<<PKGBUILDDIR>>/test/stat/12_2reads.bed | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_ok.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4
/<<PKGBUILDDIR>>/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4
/<<PKGBUILDDIR>>/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4
/<<PKGBUILDDIR>>/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam -b /tmp/4ElzIUaeY_ - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -r -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -cp -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a_regex.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b_regex.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/ziD2sgGUfK/merge.tag.1.bam /tmp/ziD2sgGUfK/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/ziD2sgGUfK/merge.tag.3.bam /tmp/ziD2sgGUfK/merge.tag.4.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge --no-PG -O SAM - /<<PKGBUILDDIR>>/test/merge/test_no_pg_rg_co.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge --no-PG -O SAM -L /<<PKGBUILDDIR>>/test/merge/merge.bed - /tmp/ziD2sgGUfK/merge.bed.1.bam /tmp/ziD2sgGUfK/merge.bed.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam -b /tmp/IApD0apZfI - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -r -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -cp -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a_regex.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b_regex.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/ziD2sgGUfK/merge.tag.1.bam /tmp/ziD2sgGUfK/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/ziD2sgGUfK/merge.tag.3.bam /tmp/ziD2sgGUfK/merge.tag.4.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 --no-PG -O SAM - /<<PKGBUILDDIR>>/test/merge/test_no_pg_rg_co.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 --no-PG -O SAM -L /<<PKGBUILDDIR>>/test/merge/merge.bed - /tmp/ziD2sgGUfK/merge.bed.1.bam /tmp/ziD2sgGUfK/merge.bed.2.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/ziD2sgGUfK/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/ziD2sgGUfK/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/ziD2sgGUfK/sorttmp
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -n -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -n -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -t AS -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -t FI -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/ziD2sgGUfK/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/ziD2sgGUfK/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/ziD2sgGUfK/sorttmp
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -n -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -n -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -t AS -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -t FI -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam -O /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -o /<<PKGBUILDDIR>>/test/collate/collate1.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -o /<<PKGBUILDDIR>>/test/collate/collate2.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate2.tmp
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate3.tmp
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam -f /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/1_fast_collate.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam -f -r 4 /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/2_fast_collate_with_tmp.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam -O /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 -o /<<PKGBUILDDIR>>/test/collate/collate1.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 -o /<<PKGBUILDDIR>>/test/collate/collate2.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate2.tmp
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate3.tmp
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam -f /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/1_fast_collate.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam -f -r 4 /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/2_fast_collate_with_tmp.sam
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/1_coord_sort.sam -
ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
.. expected failure
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/2_isize_overflow.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -cO sam /<<PKGBUILDDIR>>/test/fixmate/5_ct.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -cO sam /<<PKGBUILDDIR>>/test/fixmate/6_ct_replace.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/7_two_read_mapped.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/8_isize_overflow_64bit.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/1_coord_sort.sam -
ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
.. expected failure
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/2_isize_overflow.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -cO sam /<<PKGBUILDDIR>>/test/fixmate/5_ct.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -cO sam /<<PKGBUILDDIR>>/test/fixmate/6_ct_replace.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/7_two_read_mapped.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/8_isize_overflow_64bit.sam -
.. ok
/<<PKGBUILDDIR>>/samtools calmd -uAr /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa
.. ok
/<<PKGBUILDDIR>>/samtools calmd -@ 2 -uAr /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa
.. ok
test_idxstat:
/<<PKGBUILDDIR>>/samtools idxstats /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_idxstat:
/<<PKGBUILDDIR>>/samtools idxstats /<<PKGBUILDDIR>>/test/dat/test_input_1_a.cram
.. ok
test_idxstat:
/<<PKGBUILDDIR>>/samtools idxstats /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/1.quickcheck.badeof.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/2.quickcheck.badheader.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/3.quickcheck.ok.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/4.quickcheck.ok.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/5.quickcheck.scramble30.truncated.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/6.quickcheck.cram21.ok.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/7.quickcheck.cram30.ok.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/8.quickcheck.cram21.truncated.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/9.quickcheck.cram30.truncated.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/10.quickcheck.notargets.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck -v /<<PKGBUILDDIR>>/test/quickcheck/1.quickcheck.badeof.bam /<<PKGBUILDDIR>>/test/quickcheck/2.quickcheck.badheader.bam /<<PKGBUILDDIR>>/test/quickcheck/3.quickcheck.ok.bam /<<PKGBUILDDIR>>/test/quickcheck/4.quickcheck.ok.bam /<<PKGBUILDDIR>>/test/quickcheck/5.quickcheck.scramble30.truncated.cram /<<PKGBUILDDIR>>/test/quickcheck/6.quickcheck.cram21.ok.cram /<<PKGBUILDDIR>>/test/quickcheck/7.quickcheck.cram30.ok.cram /<<PKGBUILDDIR>>/test/quickcheck/8.quickcheck.cram21.truncated.cram /<<PKGBUILDDIR>>/test/quickcheck/9.quickcheck.cram30.truncated.cram /<<PKGBUILDDIR>>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck -uv /<<PKGBUILDDIR>>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.bam | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader --in-place /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram && /<<PKGBUILDDIR>>/samtools view -h --no-PG /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader --in-place /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram && /<<PKGBUILDDIR>>/samtools view -h --no-PG /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<<PKGBUILDDIR>>/test/dat/view.001.tmp.bam | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m overwrite_all /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m orphan_only /<<PKGBUILDDIR>>/test/addrprg/2_fixup_orphan.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -R '1#9' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m overwrite_all /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m orphan_only /<<PKGBUILDDIR>>/test/addrprg/2_fixup_orphan.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -R '1#9' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/1_name_sort.sam -
ERR: [markdup] error: queryname sorted, must be sorted by coordinate.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/2_bad_order.sam -
ERR: [markdup] error: not in coordinate sorted order.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/3_missing_mc.sam -
ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first.
[markdup] error: unable to assign pair hash key.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/4_missing_ms.sam -
ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first.
[markdup] error: no ms score tag. Please run samtools fixmate on file first.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/5_markdup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam -r --no-PG /<<PKGBUILDDIR>>/test/markdup/6_remove_dups.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/7_mark_supp_dup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/8_optical_dup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/9_optical_dup_qcfail.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/1_name_sort.sam -
ERR: [markdup] error: queryname sorted, must be sorted by coordinate.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/2_bad_order.sam -
ERR: [markdup] error: not in coordinate sorted order.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/3_missing_mc.sam -
ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first.
[markdup] error: unable to assign pair hash key.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/4_missing_ms.sam -
ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first.
[markdup] error: no ms score tag. Please run samtools fixmate on file first.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/5_markdup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam -r --no-PG /<<PKGBUILDDIR>>/test/markdup/6_remove_dups.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/7_mark_supp_dup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/8_optical_dup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/9_optical_dup_qcfail.sam -
.. ok
test_bedcov:
/<<PKGBUILDDIR>>/samtools bedcov /<<PKGBUILDDIR>>/test/bedcov/bedcov.bed /<<PKGBUILDDIR>>/test/bedcov/bedcov.bam
.. ok
test_bedcov:
/<<PKGBUILDDIR>>/samtools bedcov -j /<<PKGBUILDDIR>>/test/bedcov/bedcov.bed /<<PKGBUILDDIR>>/test/bedcov/bedcov.bam
.. ok
test_bedcov:
/<<PKGBUILDDIR>>/samtools bedcov -g512 -G2048 /<<PKGBUILDDIR>>/test/bedcov/bedcov_gG.bed /<<PKGBUILDDIR>>/test/bedcov/bedcov.bam
.. ok
test_split:
/<<PKGBUILDDIR>>/samtools split --output-fmt sam -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok
test_split:
/<<PKGBUILDDIR>>/samtools split -@ 2 --output-fmt sam -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools view -h --no-PG /tmp/ziD2sgGUfK/longref.sam.gz
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools view -h --no-PG /tmp/ziD2sgGUfK/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools view -h --no-PG -L /<<PKGBUILDDIR>>/test/large_pos/test.bed /tmp/ziD2sgGUfK/longref.sam.gz
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools sort -O sam --no-PG -m 10M /<<PKGBUILDDIR>>/test/large_pos/longref_name.sam
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools merge -O sam --no-PG - /<<PKGBUILDDIR>>/test/large_pos/longref.sam /<<PKGBUILDDIR>>/test/large_pos/longref2.sam
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools depth /<<PKGBUILDDIR>>/test/large_pos/longref.sam
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools depth -b /<<PKGBUILDDIR>>/test/large_pos/test.bed /<<PKGBUILDDIR>>/test/large_pos/longref.sam
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/ziD2sgGUfK/longref.sam.gz
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam |
/<<PKGBUILDDIR>>/samtools fixmate -O sam --no-PG - - |
/<<PKGBUILDDIR>>/samtools sort -O sam --no-PG -m 10M
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/2_both_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/2_both_test_data.sam
.. ok
test_ampliconstats:
/<<PKGBUILDDIR>>/samtools ampliconstats -@ 2 -t 50 -d 1,20,100 /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_hard_clipped.expected.sam /<<PKGBUILDDIR>>/test/ampliconclip/1_soft_clipped.expected.sam /<<PKGBUILDDIR>>/test/ampliconclip/1_soft_clipped_strand.expected.sam /<<PKGBUILDDIR>>/test/ampliconclip/2_both_clipped.expected.sam | egrep -v 'Samtools version|Command line' | tee /tmp/out.txt
.. ok
Number of tests:
total .. 700
passed .. 654
failed .. 0
expected failure .. 46
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && AWK="mawk" ./regression.sh mpileup.reg
=== Testing mpileup.reg regressions ===
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam
Expected passes: 163
Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
cd test/mpileup && AWK="mawk" ./regression.sh depth.reg
=== Testing depth.reg regressions ===
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools depth -a -b xx.bed3 xx#depth3.bam
Expected passes: 47
Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -fr -- /tmp/dh-xdg-rundir-FWXniWl9
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
rm -f -- debian/samtools.substvars
rm -fr -- debian/.debhelper/generated/samtools/ debian/samtools/ debian/tmp/
rm -f debian/samtools.debhelper.log
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install -- \
prefix=/usr
install -d /<<PKGBUILDDIR>>/debian/tmp
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
make[2]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp/usr/bin /<<PKGBUILDDIR>>/debian/tmp/usr/bin /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
install -p samtools /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl misc/plot-ampliconstats /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p -m 644 doc/samtools*.1 misc/wgsim.1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd test/dat && rm -f test_input_*.bam.bai
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o
rm -f samtools libbam.a libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/samtools.debhelper.log
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
install -d debian/samtools//usr
cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
install -d debian/samtools//usr/share/man
cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
install -d debian/samtools/usr/share/commonwl/
cp --reflink=auto -a ./debian/samtools-faidx.cwl ./debian/samtools-index.cwl ./debian/samtools-rmdup.cwl ./debian/samtools-sort.cwl ./debian/samtools-view.cwl debian/samtools/usr/share/commonwl//
cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
install -d debian/.debhelper/generated/samtools
install -d debian/.debhelper/generated/samtools-test
# Fix Perl interpreter PATH
for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \
sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a ./AUTHORS debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a ./README debian/samtools/usr/share/doc/samtools
chmod -R u\+rw,go=rX debian/samtools/usr/share/doc
install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
rm -f debian/samtools.debhelper.log
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs NEWS
install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian
install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installexamples -a
install -d debian/samtools/usr/share/doc/samtools/examples
cp --reflink=auto -a ./examples/00README.txt debian/samtools/usr/share/doc/samtools/examples
cp --reflink=auto -a ./examples/ex1.fa debian/samtools/usr/share/doc/samtools/examples
cp --reflink=auto -a ./examples/ex1.sam.gz debian/samtools/usr/share/doc/samtools/examples
cp --reflink=auto -a ./examples/toy.fa debian/samtools/usr/share/doc/samtools/examples
cp --reflink=auto -a ./examples/toy.sam debian/samtools/usr/share/doc/samtools/examples
dh_installman -a
rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1
ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1
man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-coverage.1
man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1
man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1
man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1
mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1
mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1
mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1
mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1
mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1
mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1
mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1
mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1
mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1
chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1
mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1
mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1
mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1
mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1
mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1
mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1
mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1
mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1
mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1
chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-coverage.1
mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1
mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1
mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1
mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1
mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1
mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1
mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1
mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1
mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1
chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1
mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1
mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1
mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1
mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1
mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1
mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1
mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1
mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1
mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1
chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1
dh_lintian -a
install -d debian/samtools/usr/share/lintian/overrides
install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a
(grep -a -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl:any) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a
rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1
ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1
dh_strip_nondeterminism -a
Using 1601563342 as canonical time
Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip
dh_compress -a
cd debian/samtools
chmod a-x usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
gzip -9nf usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/<<PKGBUILDDIR>>'
rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz
ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz
dh_fixperms -a
find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools -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/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing -a
dh_dwz -a -a
install -d debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -mdebian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim
dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 607205 new size 631232
objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
dh_strip -a -a
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/99a18bc488a056b51c84fde6332e49ae3dce38.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/99a18bc488a056b51c84fde6332e49ae3dce38.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/99a18bc488a056b51c84fde6332e49ae3dce38.debug debian/samtools/usr/bin/samtools
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4f
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4f/3456c2810369722857c462afb325dc2a24c531.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4f/3456c2810369722857c462afb325dc2a24c531.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4f/3456c2810369722857c462afb325dc2a24c531.debug debian/samtools/usr/bin/ace2sam
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bf
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bf/568959a1b644ab18e83098968f37bc43c13af8.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bf/568959a1b644ab18e83098968f37bc43c13af8.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bf/568959a1b644ab18e83098968f37bc43c13af8.debug debian/samtools/usr/bin/maq2sam-long
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/445cfca68b09a8881ba9f0131088997a87f023.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/445cfca68b09a8881ba9f0131088997a87f023.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/445cfca68b09a8881ba9f0131088997a87f023.debug debian/samtools/usr/bin/maq2sam-short
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/61
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/61/65decaf68a0ec5727a12284736ad93450f07ce.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/61/65decaf68a0ec5727a12284736ad93450f07ce.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/61/65decaf68a0ec5727a12284736ad93450f07ce.debug debian/samtools/usr/bin/md5fa
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5a
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5a/db80d4e5f53d72e82818bfeebcee0af6a44147.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5a/db80d4e5f53d72e82818bfeebcee0af6a44147.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5a/db80d4e5f53d72e82818bfeebcee0af6a44147.debug debian/samtools/usr/bin/md5sum-lite
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/03
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/03/d19f6740ad20c676cc2cdd7ecca56e7ffedd8e.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/03/d19f6740ad20c676cc2cdd7ecca56e7ffedd8e.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/03/d19f6740ad20c676cc2cdd7ecca56e7ffedd8e.debug debian/samtools/usr/bin/wgsim
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/samtools/usr/lib/debug/.dwz
rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug
install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -a
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -a
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=03d19f6740ad20c676cc2cdd7ecca56e7ffedd8e 4f3456c2810369722857c462afb325dc2a24c531 5adb80d4e5f53d72e82818bfeebcee0af6a44147 6165decaf68a0ec5727a12284736ad93450f07ce 67445cfca68b09a8881ba9f0131088997a87f023 ad99a18bc488a056b51c84fde6332e49ae3dce38 bf568959a1b644ab18e83098968f37bc43c13af8" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined
chmod 0644 -- debian/samtools/DEBIAN/control
dh_md5sums -a
cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/samtools/DEBIAN/md5sums
cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --root-owner-group --build debian/samtools ..
dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root ..
dpkg-deb: building package 'samtools' in '../samtools_1.11-1_armhf.deb'.
dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.11-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../samtools_1.11-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from samtools-1.11/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-10-07T09:01:23Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
samtools_1.11-1_armhf.changes:
------------------------------
Format: 1.8
Date: Thu, 01 Oct 2020 16:42:22 +0200
Source: samtools
Binary: samtools samtools-dbgsym
Architecture: armhf
Version: 1.11-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
samtools - processing sequence alignments in SAM, BAM and CRAM formats
Changes:
samtools (1.11-1) unstable; urgency=medium
.
* New upstream version
* Versioned Build-Depends: libhts-dev (>= 1.11)
Checksums-Sha1:
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f4f9de7f16b524da052fd1aa8591fe3eb9537fdf 5645 samtools_1.11-1_armhf.buildinfo
cbd39feb83780e96db9d991a103a6c3283bb4468 502280 samtools_1.11-1_armhf.deb
Checksums-Sha256:
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ae279193ba6027d9162ac37804cdb13ec235c2335113341d0a8ccc67106e49b3 5645 samtools_1.11-1_armhf.buildinfo
ae203451931e66aedab79676df8070e1a4eaf9bae959b46403a6a72fde90e0cb 502280 samtools_1.11-1_armhf.deb
Files:
85eefb3c5e8b784347dfec9451b1a6b9 779148 debug optional samtools-dbgsym_1.11-1_armhf.deb
a0336390be687be57e8ea31e58a77861 5645 science optional samtools_1.11-1_armhf.buildinfo
157c1033403f75c70bc8aca01c7f5341 502280 science optional samtools_1.11-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
samtools-dbgsym_1.11-1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 779148 bytes: control archive=900 bytes.
618 bytes, 12 lines control
830 bytes, 8 lines md5sums
Package: samtools-dbgsym
Source: samtools
Version: 1.11-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 852
Depends: samtools (= 1.11-1)
Section: debug
Priority: optional
Description: debug symbols for samtools
Build-Ids: 03d19f6740ad20c676cc2cdd7ecca56e7ffedd8e 4f3456c2810369722857c462afb325dc2a24c531 5adb80d4e5f53d72e82818bfeebcee0af6a44147 6165decaf68a0ec5727a12284736ad93450f07ce 67445cfca68b09a8881ba9f0131088997a87f023 ad99a18bc488a056b51c84fde6332e49ae3dce38 bf568959a1b644ab18e83098968f37bc43c13af8
drwxr-xr-x root/root 0 2020-10-01 14:42 ./
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/debug/.build-id/03/
-rw-r--r-- root/root 22304 2020-10-01 14:42 ./usr/lib/debug/.build-id/03/d19f6740ad20c676cc2cdd7ecca56e7ffedd8e.debug
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/debug/.build-id/4f/
-rw-r--r-- root/root 23204 2020-10-01 14:42 ./usr/lib/debug/.build-id/4f/3456c2810369722857c462afb325dc2a24c531.debug
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/debug/.build-id/5a/
-rw-r--r-- root/root 7460 2020-10-01 14:42 ./usr/lib/debug/.build-id/5a/db80d4e5f53d72e82818bfeebcee0af6a44147.debug
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/debug/.build-id/61/
-rw-r--r-- root/root 10480 2020-10-01 14:42 ./usr/lib/debug/.build-id/61/65decaf68a0ec5727a12284736ad93450f07ce.debug
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/debug/.build-id/67/
-rw-r--r-- root/root 11152 2020-10-01 14:42 ./usr/lib/debug/.build-id/67/445cfca68b09a8881ba9f0131088997a87f023.debug
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/debug/.build-id/ad/
-rw-r--r-- root/root 761156 2020-10-01 14:42 ./usr/lib/debug/.build-id/ad/99a18bc488a056b51c84fde6332e49ae3dce38.debug
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root 11156 2020-10-01 14:42 ./usr/lib/debug/.build-id/bf/568959a1b644ab18e83098968f37bc43c13af8.debug
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 3236 2020-10-01 14:42 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-10-01 14:42 ./usr/share/doc/samtools-dbgsym -> samtools
samtools_1.11-1_armhf.deb
-------------------------
new Debian package, version 2.0.
size 502280 bytes: control archive=2776 bytes.
891 bytes, 18 lines control
5090 bytes, 75 lines md5sums
Package: samtools
Version: 1.11-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1082
Depends: libc6 (>= 2.29), libhts3 (>= 1.11), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.2.3.3)
Suggests: cwltool
Breaks: bio-tradis (<= 1.4.5+dfsg-1), iva (<= 1.0.9+ds-6)
Section: science
Priority: optional
Homepage: http://www.htslib.org/
Description: processing sequence alignments in SAM, BAM and CRAM formats
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) and CRAM formats, does sorting, merging and indexing,
and allows one to retrieve reads in any regions swiftly. It is designed to work
on a stream, and is able to open a BAM or CRAM (not SAM) file on a remote FTP
or HTTP server.
drwxr-xr-x root/root 0 2020-10-01 14:42 ./
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/bin/
-rwxr-xr-x root/root 18012 2020-10-01 14:42 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5443 2020-10-01 14:42 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3360 2020-10-01 14:42 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 17996 2020-10-01 14:42 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6121 2020-10-01 14:42 ./usr/bin/interpolate_sam.pl
-rwxr-xr-x root/root 9820 2020-10-01 14:42 ./usr/bin/maq2sam-long
-rwxr-xr-x root/root 9820 2020-10-01 14:42 ./usr/bin/maq2sam-short
-rwxr-xr-x root/root 9820 2020-10-01 14:42 ./usr/bin/md5fa
-rwxr-xr-x root/root 5724 2020-10-01 14:42 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 7969 2020-10-01 14:42 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 42985 2020-10-01 14:42 ./usr/bin/plot-ampliconstats
-rwxr-xr-x root/root 50473 2020-10-01 14:42 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3204 2020-10-01 14:42 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8957 2020-10-01 14:42 ./usr/bin/sam2vcf.pl
-rwxr-xr-x root/root 525840 2020-10-01 14:42 ./usr/bin/samtools
-rwxr-xr-x root/root 16474 2020-10-01 14:42 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11327 2020-10-01 14:42 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3905 2020-10-01 14:42 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 18052 2020-10-01 14:42 ./usr/bin/wgsim
-rwxr-xr-x root/root 12542 2020-10-01 14:42 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3579 2020-10-01 14:42 ./usr/bin/zoom2sam.pl
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/commonwl/
-rwxr-xr-x root/root 1906 2020-10-01 14:42 ./usr/share/commonwl/samtools-faidx.cwl
-rwxr-xr-x root/root 1979 2020-10-01 14:42 ./usr/share/commonwl/samtools-index.cwl
-rwxr-xr-x root/root 1627 2020-10-01 14:42 ./usr/share/commonwl/samtools-rmdup.cwl
-rwxr-xr-x root/root 2834 2020-10-01 14:42 ./usr/share/commonwl/samtools-sort.cwl
-rwxr-xr-x root/root 6224 2020-10-01 14:42 ./usr/share/commonwl/samtools-view.cwl
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2020-09-22 12:15 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 369 2020-10-01 14:42 ./usr/share/doc/samtools/NEWS.Debian.gz
-rw-r--r-- root/root 4030 2020-09-22 12:15 ./usr/share/doc/samtools/README
-rw-r--r-- root/root 497 2020-10-01 14:42 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 5588 2020-10-01 14:42 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 24172 2020-09-22 12:15 ./usr/share/doc/samtools/changelog.gz
-rw-r--r-- root/root 2250 2020-10-01 14:42 ./usr/share/doc/samtools/copyright
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 1315 2020-09-22 12:15 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 3225 2020-09-22 12:15 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2020-10-01 14:42 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 98 2020-09-22 12:15 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2020-09-22 12:15 ./usr/share/doc/samtools/examples/toy.sam
drwxr-xr-x root/root 0 2020-10-01 14:42 ./usr/share/lintian/
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 24048
Build-Time: 233
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 307
Job: samtools_1.11-1
Machine Architecture: armhf
Package: samtools
Package-Time: 559
Source-Version: 1.11-1
Space: 24048
Status: successful
Version: 1.11-1
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Finished at 2020-10-07T09:01:23Z
Build needed 00:09:19, 24048k disk space