samtools →
1.9-5 →
armhf → 2019-08-19 12:52:48
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| samtools 1.9-5 (armhf) Mon, 19 Aug 2019 12:15:55 +0000 |
+==============================================================================+
Package: samtools
Version: 1.9-5
Source Version: 1.9-5
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-321bf47f-dd89-444e-91f8-9a71afe938f0' 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 [11.4 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.0 MB]
Fetched 24.5 MB in 28s (862 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 4122 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main samtools 1.9-5 (dsc) [2444 B]
Get:2 http://172.17.0.1/private bullseye-staging/main samtools 1.9-5 (tar) [4099 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main samtools 1.9-5 (diff) [20.8 kB]
Fetched 4122 kB in 0s (9064 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/samtools-lCBO9B/samtools-1.9' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/samtools-lCBO9B' 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-je47jq/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-je47jq/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-je47jq/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-je47jq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-je47jq/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-je47jq/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-je47jq/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-je47jq/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2817 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 87 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-je47jq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12050 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-amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.9), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0)
Filtered Build-Depends: debhelper-compat (= 12), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.9), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0)
dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/<<BUILDDIR>>/resolver-je47jq/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-je47jq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-je47jq/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-je47jq/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-je47jq/apt_archive ./ Sources [582 B]
Get:5 copy:/<<BUILDDIR>>/resolver-je47jq/apt_archive ./ Packages [654 B]
Fetched 2569 B in 1s (3268 B/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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bash-completion
bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file
gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
libcroco3 libcurl3-gnutls libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgnutls30 libgssapi-krb5-2
libhts-dev libhts2 libicu63 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 libtasn1-6
libtinfo5 libtinfo6 libtool libuchardet0 libxml2 m4 man-db pkg-config
po-debconf sensible-utils tabix zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin 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 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
bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file
gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
libcroco3 libcurl3-gnutls libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
libhts2 libicu63 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 libtinfo5 libtool
libuchardet0 libxml2 m4 man-db pkg-config po-debconf
sbuild-build-depends-samtools-dummy sensible-utils tabix zlib1g-dev
The following packages will be upgraded:
libgnutls30 libncursesw6 libtasn1-6 libtinfo6
4 upgraded, 59 newly installed, 0 to remove and 83 not upgraded.
Need to get 29.1 MB of archives.
After this operation, 90.8 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-je47jq/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [944 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20190803-1 [314 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.8.6.1-1 [1248 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf autoconf-archive all 20180313-1 [749 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libtasn1-6 armhf 4.14-2 [48.2 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libgnutls30 armhf 3.6.9-4 [1081 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.1+20190803-1 [318 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.1+20190803-1 [104 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf bash-completion all 1:2.8-6 [208 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-5 [253 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-5 [111 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-5 [66.2 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.5.0-1 [22.8 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.5.0-1 [14.1 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-1 [69.7 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.60.6-2 [1109 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b2 [571 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20190803-1 [79.3 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.4 [1029 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1c-1 [1259 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.39.2-1 [71.3 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.65.3-1 [298 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.2-1 [48.4 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-11 [255 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.9-11 [4286 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libio-pty-perl armhf 1:1.08-1.1+b4 [33.0 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.1+20190803-1 [281 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.1+20190803-1 [940 B]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf tabix armhf 1.9-11 [241 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking dh-strip-nondeterminism (1.5.0-1) ...
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Unpacking libglib2.0-0:armhf (2.60.6-2) ...
Selecting previously unselected package libicu63:armhf.
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Unpacking libicu63:armhf (63.2-2) ...
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Unpacking libxml2:armhf (2.9.4+dfsg1-7+b2) ...
Selecting previously unselected package libcroco3:armhf.
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Unpacking libcroco3:armhf (0.6.12-3) ...
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Unpacking gettext (0.19.8.1-9) ...
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Selecting previously unselected package po-debconf.
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Unpacking po-debconf (1.0.21) ...
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Unpacking debhelper (12.4) ...
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Unpacking libkeyutils1:armhf (1.6-6) ...
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Unpacking libkrb5support0:armhf (1.17-6+b1) ...
Selecting previously unselected package libk5crypto3:armhf.
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Unpacking libk5crypto3:armhf (1.17-6+b1) ...
Selecting previously unselected package libssl1.1:armhf.
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Unpacking libssl1.1:armhf (1.1.1c-1) ...
Selecting previously unselected package libkrb5-3:armhf.
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Unpacking libkrb5-3:armhf (1.17-6+b1) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
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Unpacking libgssapi-krb5-2:armhf (1.17-6+b1) ...
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Unpacking libnghttp2-14:armhf (1.39.2-1) ...
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Unpacking libpsl5:armhf (0.20.2-2) ...
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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Selecting previously unselected package libssh2-1:armhf.
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Unpacking libssh2-1:armhf (1.8.0-2.1) ...
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Unpacking libcurl3-gnutls:armhf (7.65.3-1) ...
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Unpacking libdeflate0:armhf (1.2-1) ...
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Unpacking libhts2:armhf (1.9-11) ...
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Unpacking liblzma-dev:armhf (5.2.4-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
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Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
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Unpacking libhts-dev:armhf (1.9-11) ...
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Unpacking libio-pty-perl (1:1.08-1.1+b4) ...
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Unpacking tabix (1.9-11) ...
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Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up libkeyutils1:armhf (1.6-6) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libio-pty-perl (1:1.08-1.1+b4) ...
Setting up libmagic-mgc (1:5.37-5) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libglib2.0-0:armhf (2.60.6-2) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1c-1) ...
Setting up libnghttp2-14:armhf (1.39.2-1) ...
Setting up libmagic1:armhf (1:5.37-5) ...
Setting up libdeflate0:armhf (1.2-1) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up autoconf-archive (20180313-1) ...
Setting up file (1:5.37-5) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up autotools-dev (20180224.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up bash-completion (1:2.8-6) ...
Setting up libncurses6:armhf (6.1+20190803-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up pkg-config (0.29-6) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20190803-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b2) ...
Setting up libfile-stripnondeterminism-perl (1.5.0-1) ...
Setting up libncurses-dev:armhf (6.1+20190803-1) ...
Setting up libtool (2.4.6-9) ...
Setting up m4 (1.4.18-2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.13-1) ...
Setting up groff-base (1.22.4-3) ...
Setting up libncurses5-dev:armhf (6.1+20190803-1) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-9) ...
Setting up libcurl3-gnutls:armhf (7.65.3-1) ...
Setting up man-db (2.8.6.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up tabix (1.9-11) ...
Setting up libhts2:armhf (1.9-11) ...
Setting up po-debconf (1.0.21) ...
Setting up libhts-dev:armhf (1.9-11) ...
Setting up debhelper (12.4) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.5.0-1) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-10+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-16+rpi1 dpkg-dev_1.19.7 g++-8_8.3.0-6+rpi1 gcc-8_8.3.0-6+rpi1 libc6-dev_2.28-10+rpi1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 autoconf-archive_20180313-1 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3+rpi1 base-passwd_3.5.46 bash_5.0-4 bash-completion_1:2.8-6 binutils_2.31.1-16+rpi1 binutils-arm-linux-gnueabihf_2.31.1-16+rpi1 binutils-common_2.31.1-16+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9.1 coreutils_8.30-3 cpp_4:8.3.0-1+rpi2 cpp-8_8.3.0-6+rpi1 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.4 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.5.0-1 diffutils_1:3.7-3 dirmngr_2.2.12-1+rpi1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.37-5 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1+rpi2 g++-8_8.3.0-6+rpi1 gcc_4:8.3.0-1+rpi2 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b1 gcc-7-base_7.3.0-19 gcc-8_8.3.0-6+rpi1 gcc-8-base_8.3.0-6+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_8.3.0-6+rpi1 libassuan0_2.5.2-1 libatomic1_8.3.0-6+rpi1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16+rpi1 libblkid1_2.33.1-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.6-9.1 libc-bin_2.28-10+rpi1 libc-dev-bin_2.28-10+rpi1 libc6_2.28-10+rpi1 libc6-dev_2.28-10+rpi1 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-6+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcurl3-gnutls_7.65.3-1 libdb5.3_5.3.28+dfsg1-0.5 libdebconfclient0_0.249 libdeflate0_1.2-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.5.0-1 libgcc-8-dev_8.3.0-6+rpi1 libgcc1_1:8.3.0-6+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libglib2.0-0_2.60.6-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-4 libgomp1_8.3.0-6+rpi1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-6+b1 libhogweed4_3.4.1-1 libhts-dev_1.9-11 libhts2_1.9-11 libicu63_63.2-2 libidn2-0_2.0.5-1 libio-pty-perl_1:1.08-1.1+b4 libisl19_0.20-2 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblocale-gettext-perl_1.07-3+b3 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.1+20190803-1 libncurses5-dev_6.1+20190803-1 libncurses6_6.1+20190803-1 libncursesw6_6.1+20190803-1 libnettle6_3.4.1-1 libnghttp2-14_1.39.2-1 libnpth0_1.6-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpsl5_0.20.2-2 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.27.2-3 libss2_1.44.5-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_241-5+rpi1 libtasn1-6_4.14-2 libtext-charwidth-perl_0.04-7.1+b1 libtext-iconv-perl_1.7-5+b10 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20190803-1 libtinfo6_6.1+20190803-1 libtool_2.4.6-9 libubsan1_8.3.0-6+rpi1 libuchardet0_0.0.6-3 libudev1_241-5+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b2 libzstd1_1.3.8+dfsg-3+rpi1 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2019051400+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.6.1-1 mawk_1.3.3-17 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 pkg-config_0.29-6 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 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 sysvinit-utils_2.93-8 tabix_1.9-11 tar_1.30+dfsg-6 tzdata_2019a-1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Aug 17 08:21:07 2019 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./samtools_1.9-5.dsc
dpkg-source: info: extracting samtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking samtools_1.9.orig.tar.gz
dpkg-source: info: unpacking samtools_1.9-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying sort-tests-memory-limit.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-321bf47f-dd89-444e-91f8-9a71afe938f0
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package samtools
dpkg-buildpackage: info: source version 1.9-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from samtools-1.9/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot 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 --
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 build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p
" > debian/autoreconf.before
grep -q ^XDT_ configure.ac
autoreconf -f -i
configure.ac:56: 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:56: the top level
configure.ac:56: 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:56: the top level
configure.ac:56: 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:56: the top level
configure.ac:56: 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:56: 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:56: 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:56: the top level
autoconf
configure.ac:56: 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:56: the top level
dh_auto_configure -- --with-htslib=system
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
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 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 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_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 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 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 "1.9"' > 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 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 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 bam_import.o bam_import.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 sam_header.o sam_header.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 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 bam_import.o sam.o sam_header.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
gcc -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -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/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_rtrans_build test/merge/test_rtrans_build.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 libst.a -lhts -lz -lpthread
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/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_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.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 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 ./lz4/lz4.o libbam.a libst.a -lhts -lcurses -lm -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
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>>'
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-}
/usr/bin/bgzip -c -b 65272 -s 5 /tmp/iI_swwqwqc/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 979200 -s 6 /tmp/iI_swwqwqc/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 652804 -s 6 /tmp/iI_swwqwqc/bgzip.dat.gz
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/iI_swwqwqc/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/iI_swwqwqc/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/iI_swwqwqc/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/iI_swwqwqc/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/iI_swwqwqc/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/iI_swwqwqc/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/iI_swwqwqc/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/iI_swwqwqc/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/iI_swwqwqc/fqidx.fq 3:11-13
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/iI_swwqwqc/fqidx.fq.gz 3:11-13
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/iI_swwqwqc/fqidx.fq 2:998-1003
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/iI_swwqwqc/fqidx.fq.gz 2:998-1003
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/iI_swwqwqc/fqidx.fq 1:100-104
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/iI_swwqwqc/fqidx.fq.gz 1:100-104
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/iI_swwqwqc/fqidx.fq 1:99998-100007
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/iI_swwqwqc/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/iI_swwqwqc/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_index:
/<<PKGBUILDDIR>>/samtools view /tmp/iI_swwqwqc/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view /tmp/iI_swwqwqc/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 -@ 2 /tmp/iI_swwqwqc/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/iI_swwqwqc/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_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/iI_swwqwqc/mpileup.bam.list -f /tmp/iI_swwqwqc/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/iI_swwqwqc/mpileup.cram.list -f /tmp/iI_swwqwqc/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/iI_swwqwqc/mpileup.bam.urllist -f /tmp/iI_swwqwqc/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/iI_swwqwqc/mpileup.cram.urllist -f /tmp/iI_swwqwqc/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/iI_swwqwqc/mpileup.bam.list -f /tmp/iI_swwqwqc/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/iI_swwqwqc/mpileup.cram.list -f /tmp/iI_swwqwqc/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/iI_swwqwqc/mpileup.cram.list -f /tmp/iI_swwqwqc/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/iI_swwqwqc/mpileup.cram.list -f /tmp/iI_swwqwqc/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/iI_swwqwqc/mpileup.ref.fa.gz -r17:1050-1060 /tmp/iI_swwqwqc/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/iI_swwqwqc/mpileup.ref.fa.gz -r17:1050-1060 /tmp/iI_swwqwqc/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, 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 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 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 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/iI_swwqwqc/view.001.fogn (SAM input) .. ok
50: Count -R /tmp/iI_swwqwqc/view.001.fogn (SAM input) .. ok
51: Filter -R /tmp/iI_swwqwqc/view.001.fogn (BAM input) .. ok
52: Count -R /tmp/iI_swwqwqc/view.001.fogn (BAM input) .. ok
53: Filter -R /tmp/iI_swwqwqc/view.001.fogn (CRAM input) .. ok
54: Count -R /tmp/iI_swwqwqc/view.001.fogn (CRAM input) .. ok
55: Filter -R /tmp/iI_swwqwqc/view.001.fogn -r grp2 (SAM input).. ok
56: Count -R /tmp/iI_swwqwqc/view.001.fogn -r grp2 (SAM input).. ok
57: Filter -R /tmp/iI_swwqwqc/view.001.fogn -r grp2 (BAM input).. ok
58: Count -R /tmp/iI_swwqwqc/view.001.fogn -r grp2 (BAM input).. ok
59: Filter -R /tmp/iI_swwqwqc/view.001.fogn -r grp2 (CRAM input).. ok
60: Count -R /tmp/iI_swwqwqc/view.001.fogn -r grp2 (CRAM input).. ok
61: Filter -r grp2 -R /tmp/iI_swwqwqc/view.001.fogn (SAM input).. ok
62: Count -r grp2 -R /tmp/iI_swwqwqc/view.001.fogn (SAM input).. ok
63: Filter -r grp2 -R /tmp/iI_swwqwqc/view.001.fogn (BAM input).. ok
64: Count -r grp2 -R /tmp/iI_swwqwqc/view.001.fogn (BAM input).. ok
65: Filter -r grp2 -R /tmp/iI_swwqwqc/view.001.fogn (CRAM input).. ok
66: Count -r grp2 -R /tmp/iI_swwqwqc/view.001.fogn (CRAM input).. ok
67: Filter -l Library 2 (SAM input) .. ok
68: Count -l Library 2 (SAM input) .. ok
69: Filter -l Library 2 (BAM input) .. ok
70: Count -l Library 2 (BAM input) .. ok
71: Filter -l Library 2 (CRAM input) .. ok
72: Count -l Library 2 (CRAM input) .. ok
73: Filter -l Library 3 (SAM input) .. ok
74: Count -l Library 3 (SAM input) .. ok
75: Filter -l Library 3 (BAM input) .. ok
76: Count -l Library 3 (BAM input) .. ok
77: Filter -l Library 3 (CRAM input) .. ok
78: Count -l Library 3 (CRAM input) .. ok
79: Filter -q 50 (SAM input) .. ok
80: Count -q 50 (SAM input) .. ok
81: Filter -q 50 (BAM input) .. ok
82: Count -q 50 (BAM input) .. ok
83: Filter -q 50 (CRAM input) .. ok
84: Count -q 50 (CRAM input) .. ok
85: Filter -q 99 (SAM input) .. ok
86: Count -q 99 (SAM input) .. ok
87: Filter -q 99 (BAM input) .. ok
88: Count -q 99 (BAM input) .. ok
89: Filter -q 99 (CRAM input) .. ok
90: Count -q 99 (CRAM input) .. ok
91: Filter -q 100 (SAM input) .. ok
92: Count -q 100 (SAM input) .. ok
93: Filter -q 100 (BAM input) .. ok
94: Count -q 100 (BAM input) .. ok
95: Filter -q 100 (CRAM input) .. ok
96: Count -q 100 (CRAM input) .. ok
97: Filter -x fa (SAM input) .. ok
98: Count -x fa (SAM input) .. ok
99: Filter -x fa (BAM input) .. ok
100: Count -x fa (BAM input) .. ok
101: Filter -x fa (CRAM input) .. ok
102: Count -x fa (CRAM input) .. ok
103: Filter -x fa -x ha (SAM input) .. ok
104: Count -x fa -x ha (SAM input) .. ok
105: Filter -x fa -x ha (BAM input) .. ok
106: Count -x fa -x ha (BAM input) .. ok
107: Filter -x fa -x ha (CRAM input) .. ok
108: Count -x fa -x ha (CRAM input) .. ok
109: Filter -x fa -r grp2 (SAM input) .. ok
110: Count -x fa -r grp2 (SAM input) .. ok
111: Filter -x fa -r grp2 (BAM input) .. ok
112: Count -x fa -r grp2 (BAM input) .. ok
113: Filter -x fa -r grp2 (CRAM input) .. ok
114: Count -x fa -r grp2 (CRAM input) .. ok
115: Filter -x RG -r grp2 (SAM input) .. ok
116: Count -x RG -r grp2 (SAM input) .. ok
117: Filter -x RG -r grp2 (BAM input) .. ok
118: Count -x RG -r grp2 (BAM input) .. ok
119: Filter -x RG -r grp2 (CRAM input) .. ok
120: Count -x RG -r grp2 (CRAM input) .. ok
121: Filter -m 10 (SAM input) .. ok
122: Count -m 10 (SAM input) .. ok
123: Filter -m 10 (BAM input) .. ok
124: Count -m 10 (BAM input) .. ok
125: Filter -m 10 (CRAM input) .. ok
126: Count -m 10 (CRAM input) .. ok
127: Filter -m 11 (SAM input) .. ok
128: Count -m 11 (SAM input) .. ok
129: Filter -m 11 (BAM input) .. ok
130: Count -m 11 (BAM input) .. ok
131: Filter -m 11 (CRAM input) .. ok
132: Count -m 11 (CRAM input) .. ok
133: Filter -m 15 (SAM input) .. ok
134: Count -m 15 (SAM input) .. ok
135: Filter -m 15 (BAM input) .. ok
136: Count -m 15 (BAM input) .. ok
137: Filter -m 15 (CRAM input) .. ok
138: Count -m 15 (CRAM input) .. ok
139: Filter -m 16 (SAM input) .. ok
140: Count -m 16 (SAM input) .. ok
141: Filter -m 16 (BAM input) .. ok
142: Count -m 16 (BAM input) .. ok
143: Filter -m 16 (CRAM input) .. ok
144: Count -m 16 (CRAM input) .. ok
145: 1bp reads file SAM -> BAM -> SAM .. ok
146: 1bp reads file SAM -> CRAM -> SAM .. ok
146: Region Z (BAM input) .. ok
147: Count Z (BAM input) .. ok
148: Region Z (CRAM input) .. ok
149: Count Z (CRAM input) .. ok
150: Region Z:30 (BAM input) .. ok
151: Count Z:30 (BAM input) .. ok
152: Region Z:30 (CRAM input) .. ok
153: Count Z:30 (CRAM input) .. ok
154: Region Z:20-40 (BAM input) .. ok
155: Count Z:20-40 (BAM input) .. ok
156: Region Z:20-40 (CRAM input) .. ok
157: Count Z:20-40 (CRAM input) .. ok
158: Region ref1 (BAM input) .. ok
159: Count ref1 (BAM input) .. ok
160: Region ref1 (CRAM input) .. ok
161: Count ref1 (CRAM input) .. ok
162: Region ref1:15 (BAM input) .. ok
163: Count ref1:15 (BAM input) .. ok
164: Region ref1:15 (CRAM input) .. ok
165: Count ref1:15 (CRAM input) .. ok
166: Region ref1:15-45 (BAM input) .. ok
167: Count ref1:15-45 (BAM input) .. ok
168: Region ref1:15-45 (CRAM input) .. ok
169: Count ref1:15-45 (CRAM input) .. ok
170: Region ref1:15-45 ref2 (BAM input) .. ok
171: Count ref1:15-45 ref2 (BAM input) .. ok
172: Region ref1:15-45 ref2 (CRAM input) .. ok
173: Count ref1:15-45 ref2 (CRAM input) .. ok
174: Region ref1:15-45 ref2:16 (BAM input) .. ok
175: Count ref1:15-45 ref2:16 (BAM input) .. ok
176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
186: Region -f 128 ref1 (BAM input) .. ok
187: Count -f 128 ref1 (BAM input) .. ok
188: Region -f 128 ref1 (CRAM input) .. ok
189: Count -f 128 ref1 (CRAM input) .. ok
190: Region -q 50 ref1:15-45 (BAM input) .. ok
191: Count -q 50 ref1:15-45 (BAM input) .. ok
192: Region -q 50 ref1:15-45 (CRAM input) .. ok
193: Count -q 50 ref1:15-45 (CRAM input) .. ok
194: Region -r grp2 ref1:15-45 (BAM input) .. ok
195: Count -r grp2 ref1:15-45 (BAM input) .. ok
196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
198: Region * (BAM input) .. ok
199: Count * (BAM input) .. ok
200: Region * (CRAM input) .. ok
201: Count * (CRAM input) .. ok
202: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
203: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
204: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
205: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
206: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
207: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
208: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
209: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
210: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
211: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
212: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
213: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
214: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
215: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
216: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
217: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
218: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
219: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
220: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
221: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
222: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
223: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
224: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
225: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
226: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
227: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
228: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
229: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
230: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
231: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
232: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
233: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
234: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
235: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
236: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
237: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
238: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
239: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
240: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
241: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
242: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
243: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
244: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
245: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
246: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
247: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
248: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
249: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
250: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
251: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
252: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
253: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
254: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
255: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
256: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
257: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
258: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
259: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
260: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
261: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
262: Make BAM with no M5/UR tags .. ok
263: Add @SQ with -t (SAM -> SAM) .. ok
264: Add @SQ with -T (SAM -> SAM) .. ok
265: Add @SQ with -t (BAM -> SAM) .. ok
266: Add @SQ with -T (BAM -> SAM) .. ok
267: Add @SQ with -t (SAM -> BAM) .. ok
268: Add @SQ with -T (SAM -> BAM) .. ok
269: Add @SQ with -t (BAM -> BAM) .. ok
270: Add @SQ with -T (BAM -> BAM) .. ok
271: Add @SQ with -t (SAM -> CRAM) .. ok
272: Add @SQ with -T (SAM -> CRAM) .. ok
273: Add @SQ with -t (BAM -> CRAM) .. ok
274: Add @SQ with -T (BAM -> CRAM) .. ok
275: Make CRAM with no UR field .. ok
276: Decoding CRAM with no UR field via -T .. ok
277: CIGAR B-operator removal .. ok
278: Big SAM -> BAM .. ok
279: Big SAM -> BAM (2 threads) .. ok
280: Big SAM -> BAM (4 threads) .. ok
281: Big SAM -> CRAM .. ok
282: Big SAM -> CRAM (2 threads) .. ok
283: Big SAM -> CRAM (4 threads) .. ok
284: Subsample 0.2 (SAM input) ............ ok
285: Subsample 0.5 (SAM input) ............ ok
286: Subsample 0.8 (SAM input) ............ ok
287: Subsample 0.2 (BAM input) ............ ok
288: Subsample 0.5 (BAM input) ............ ok
289: Subsample 0.8 (BAM input) ............ ok
290: Subsample 0.2 (CRAM input) ............ ok
291: Subsample 0.5 (CRAM input) ............ ok
292: Subsample 0.8 (CRAM input) ............ 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 -N -t -i -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 -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.703.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 -N -t -i -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 -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.703.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 -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/2_equal_cigar_full_seq.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 -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/4_X_cigar_full_seq.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 -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 -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/8_secondary.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_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/xNg7q9SuS1 - /<<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/iI_swwqwqc/merge.tag.1.bam /tmp/iI_swwqwqc/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/iI_swwqwqc/merge.tag.3.bam /tmp/iI_swwqwqc/merge.tag.4.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/xpayAKgw55 - /<<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/iI_swwqwqc/merge.tag.1.bam /tmp/iI_swwqwqc/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/iI_swwqwqc/merge.tag.3.bam /tmp/iI_swwqwqc/merge.tag.4.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/iI_swwqwqc/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/iI_swwqwqc/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/iI_swwqwqc/sorttmp
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -m 192M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -m 192M -n /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -m 192M -t RG /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -m 192M -n -t RG /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -m 192M -t AS /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -m 192M -t FI /<<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/iI_swwqwqc/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/iI_swwqwqc/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/iI_swwqwqc/sorttmp
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -m 192M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -m 192M -n /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -m 192M -t RG /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -m 192M -n -t RG /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -m 192M -t AS /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -m 192M -t FI /<<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 -@ 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
/<<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 -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 | 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 | 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 | 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 | 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 /<<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 /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | 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#7' /<<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#7' /<<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 /<<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 /<<PKGBUILDDIR>>/test/markdup/2_bad_order.sam -
ERR: [markdup] error: bad coordinate order.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam /<<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 /<<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 /<<PKGBUILDDIR>>/test/markdup/5_markdup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam -r /<<PKGBUILDDIR>>/test/markdup/6_remove_dups.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -O sam /<<PKGBUILDDIR>>/test/markdup/7_mark_supp_dup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam /<<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 /<<PKGBUILDDIR>>/test/markdup/2_bad_order.sam -
ERR: [markdup] error: bad coordinate order.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam /<<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 /<<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 /<<PKGBUILDDIR>>/test/markdup/5_markdup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam -r /<<PKGBUILDDIR>>/test/markdup/6_remove_dups.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -O sam /<<PKGBUILDDIR>>/test/markdup/7_mark_supp_dup.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
Number of tests:
total .. 565
passed .. 541
failed .. 0
expected failure .. 24
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 && ./regression.sh mpileup.reg
=== Testing mpileup.reg regressions ===
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -Q0 -x -f c1.fa c1#pad1.bam
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -Q0 -x -f c1.fa c1#pad2.bam
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam
Expected passes: 153
Unexpected passes: 0
Expected failures: 3
Unexpected failures: 0
=> PASS
cd test/mpileup && ./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: 43
Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
test/split/test_parse_args
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
rm -f -- debian/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/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p -m 644 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
chown -R 0:0 debian/samtools/usr/share/doc
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
man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/samtools.1 > debian/samtools/usr/share/man/man1/samtools.1.dh-new
man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/wgsim.1 > debian/samtools/usr/share/man/man1/wgsim.1.dh-new
man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/ace2sam.1 > debian/samtools/usr/share/man/man1/ace2sam.1.dh-new
man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/samtools.pl.1 > debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new
mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1
chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.pl.1
mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1
chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.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/wgsim.1
mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1
chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.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
dh_strip_nondeterminism -a
Using 1566030007 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.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.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/<<PKGBUILDDIR>>'
dh_fixperms -a
find debian/samtools -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
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
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 533498 new size 551476
objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
dh_strip -a
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2f
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2f/5d3b9529cefeddf568d43f2685c32d35abd8aa.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2f/5d3b9529cefeddf568d43f2685c32d35abd8aa.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2f/5d3b9529cefeddf568d43f2685c32d35abd8aa.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/2f/5d3b9529cefeddf568d43f2685c32d35abd8aa.debug debian/samtools/usr/bin/samtools
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0f
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0f/3ddee83a2ff5f169baf28d957181f38a314324.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0f/3ddee83a2ff5f169baf28d957181f38a314324.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0f/3ddee83a2ff5f169baf28d957181f38a314324.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/0f/3ddee83a2ff5f169baf28d957181f38a314324.debug debian/samtools/usr/bin/ace2sam
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e/89af868351ea678db178070b52f7d4d00f7e6d.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e/89af868351ea678db178070b52f7d4d00f7e6d.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6e/89af868351ea678db178070b52f7d4d00f7e6d.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/6e/89af868351ea678db178070b52f7d4d00f7e6d.debug debian/samtools/usr/bin/maq2sam-long
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ff
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ff/482ce783701c9c47e9d5c3d8408bc2ea1cbfc5.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ff/482ce783701c9c47e9d5c3d8408bc2ea1cbfc5.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ff/482ce783701c9c47e9d5c3d8408bc2ea1cbfc5.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/ff/482ce783701c9c47e9d5c3d8408bc2ea1cbfc5.debug debian/samtools/usr/bin/maq2sam-short
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e9
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e9/fd64b081b439a92934feb2954d026e37e9dc68.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e9/fd64b081b439a92934feb2954d026e37e9dc68.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e9/fd64b081b439a92934feb2954d026e37e9dc68.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/e9/fd64b081b439a92934feb2954d026e37e9dc68.debug debian/samtools/usr/bin/md5fa
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/ab5a4802dd7175add030432580e5fa81907ec8.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/ab5a4802dd7175add030432580e5fa81907ec8.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/ab5a4802dd7175add030432580e5fa81907ec8.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/cd/ab5a4802dd7175add030432580e5fa81907ec8.debug debian/samtools/usr/bin/md5sum-lite
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b7
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b7/aebd94046c530e7c8e09d712671b2842d598ea.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b7/aebd94046c530e7c8e09d712671b2842d598ea.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b7/aebd94046c530e7c8e09d712671b2842d598ea.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/b7/aebd94046c530e7c8e09d712671b2842d598ea.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
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -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/md5fa debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools 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 -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=0f3ddee83a2ff5f169baf28d957181f38a314324 2f5d3b9529cefeddf568d43f2685c32d35abd8aa 6e89af868351ea678db178070b52f7d4d00f7e6d b7aebd94046c530e7c8e09d712671b2842d598ea cdab5a4802dd7175add030432580e5fa81907ec8 e9fd64b081b439a92934feb2954d026e37e9dc68 ff482ce783701c9c47e9d5c3d8408bc2ea1cbfc5" -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
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools -UMulti-Arch
dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined
chmod 0644 -- debian/samtools/DEBIAN/control
chown 0:0 -- debian/samtools/DEBIAN/control
dh_md5sums -a
cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/samtools/DEBIAN/md5sums
chown 0:0 -- debian/samtools/DEBIAN/md5sums
cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --build debian/samtools ..
dpkg-deb --build debian/.debhelper/samtools/dbgsym-root ..
dpkg-deb: building package 'samtools' in '../samtools_1.9-5_armhf.deb'.
dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.9-5_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../samtools_1.9-5_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from samtools-1.9/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-08-19T12:52:37Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
samtools_1.9-5_armhf.changes:
-----------------------------
Format: 1.8
Date: Sat, 17 Aug 2019 10:20:07 +0200
Source: samtools
Binary: samtools samtools-dbgsym
Architecture: armhf
Version: 1.9-5
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <michael.crusoe@gmail.com>
Description:
samtools - processing sequence alignments in SAM, BAM and CRAM formats
Changes:
samtools (1.9-5) unstable; urgency=medium
.
[ Andreas Tille ]
* Use <!nocheck> for libio-pty-perl
.
[ Michael R. Crusoe ]
* Stop building on any-i386 due to htslib dropping i386
* debhelper-compat 12
* Standards-Version: 4.4.0
Checksums-Sha1:
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ad0a04df9fe7dcb090a681cd9c2e9ea2e130e9a1 5452 samtools_1.9-5_armhf.buildinfo
4e227f2b95acd5707a7a79998872de7e9c005332 396780 samtools_1.9-5_armhf.deb
Checksums-Sha256:
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ebc89b97a48af6921ff41bf729924c91b822c9f0f36a397be2fcbc2c2b79a191 5452 samtools_1.9-5_armhf.buildinfo
a118b95913bf8fb4dce5157d6176fe96ebb7413d53dcb777e5edd5d730faf2d7 396780 samtools_1.9-5_armhf.deb
Files:
666b4d7fc9f39d404a6e7c84306bb154 681128 debug optional samtools-dbgsym_1.9-5_armhf.deb
9e996b6459f56f8251ac1354ad1b933e 5452 science optional samtools_1.9-5_armhf.buildinfo
14716d73449af85244ccd8425e2b26c2 396780 science optional samtools_1.9-5_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
samtools-dbgsym_1.9-5_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 681128 bytes: control archive=896 bytes.
616 bytes, 12 lines control
830 bytes, 8 lines md5sums
Package: samtools-dbgsym
Source: samtools
Version: 1.9-5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 752
Depends: samtools (= 1.9-5)
Section: debug
Priority: optional
Description: debug symbols for samtools
Build-Ids: 0f3ddee83a2ff5f169baf28d957181f38a314324 2f5d3b9529cefeddf568d43f2685c32d35abd8aa 6e89af868351ea678db178070b52f7d4d00f7e6d b7aebd94046c530e7c8e09d712671b2842d598ea cdab5a4802dd7175add030432580e5fa81907ec8 e9fd64b081b439a92934feb2954d026e37e9dc68 ff482ce783701c9c47e9d5c3d8408bc2ea1cbfc5
drwxr-xr-x root/root 0 2019-08-17 08:20 ./
drwxr-xr-x root/root 0 2019-08-17 08:20 ./usr/
drwxr-xr-x root/root 0 2019-08-17 08:20 ./usr/lib/
drwxr-xr-x root/root 0 2019-08-17 08:20 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-08-17 08:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-08-17 08:20 ./usr/lib/debug/.build-id/0f/
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samtools_1.9-5_armhf.deb
------------------------
new Debian package, version 2.0.
size 396780 bytes: control archive=1976 bytes.
839 bytes, 17 lines control
2701 bytes, 43 lines md5sums
Package: samtools
Version: 1.9-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 886
Depends: libc6 (>= 2.7), libhts2 (>= 1.9), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python, cwltool
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.
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drwxr-xr-x root/root 0 2019-08-17 08:20 ./usr/
drwxr-xr-x root/root 0 2019-08-17 08:20 ./usr/bin/
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-rwxr-xr-x root/root 5437 2019-08-17 08:20 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3360 2019-08-17 08:20 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18028 2019-08-17 08:20 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6121 2019-08-17 08:20 ./usr/bin/interpolate_sam.pl
-rwxr-xr-x root/root 9820 2019-08-17 08:20 ./usr/bin/maq2sam-long
-rwxr-xr-x root/root 9820 2019-08-17 08:20 ./usr/bin/maq2sam-short
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-rwxr-xr-x root/root 6769 2019-08-17 08:20 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48826 2019-08-17 08:20 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3204 2019-08-17 08:20 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8957 2019-08-17 08:20 ./usr/bin/sam2vcf.pl
-rwxr-xr-x root/root 452108 2019-08-17 08:20 ./usr/bin/samtools
-rwxr-xr-x root/root 16474 2019-08-17 08:20 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11101 2019-08-17 08:20 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3905 2019-08-17 08:20 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2018-07-18 08:33 ./usr/bin/varfilter.py
-rwxr-xr-x root/root 18052 2019-08-17 08:20 ./usr/bin/wgsim
-rwxr-xr-x root/root 12536 2019-08-17 08:20 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3579 2019-08-17 08:20 ./usr/bin/zoom2sam.pl
drwxr-xr-x root/root 0 2019-08-17 08:20 ./usr/share/
drwxr-xr-x root/root 0 2019-08-17 08:20 ./usr/share/commonwl/
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-rwxr-xr-x root/root 1979 2019-08-17 08:15 ./usr/share/commonwl/samtools-index.cwl
-rwxr-xr-x root/root 1627 2019-08-17 08:15 ./usr/share/commonwl/samtools-rmdup.cwl
-rwxr-xr-x root/root 2834 2019-08-17 08:15 ./usr/share/commonwl/samtools-sort.cwl
-rwxr-xr-x root/root 6224 2019-08-17 08:15 ./usr/share/commonwl/samtools-view.cwl
drwxr-xr-x root/root 0 2019-08-17 08:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-08-17 08:20 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2018-07-18 08:33 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 369 2019-08-17 08:15 ./usr/share/doc/samtools/NEWS.Debian.gz
-rw-r--r-- root/root 4025 2018-07-18 08:33 ./usr/share/doc/samtools/README
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-rw-r--r-- root/root 3451 2019-08-17 08:20 ./usr/share/doc/samtools/copyright
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Build Architecture: armhf
Build-Space: 20100
Build-Time: 781
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 1358
Job: samtools_1.9-5
Machine Architecture: armhf
Package: samtools
Package-Time: 2202
Source-Version: 1.9-5
Space: 20100
Status: successful
Version: 1.9-5
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Finished at 2019-08-19T12:52:37Z
Build needed 00:36:42, 20100k disc space