samtools →
1.7-2 →
armhf → 2018-04-04 06:39:24
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| samtools 1.7-2 (armhf) Wed, 04 Apr 2018 06:33:16 +0000 |
+==============================================================================+
Package: samtools
Version: 1.7-2
Source Version: 1.7-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-cc93bc07-1aad-48aa-8100-f2cc2d37b36e' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.7 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.4 MB]
Fetched 23.1 MB in 12s (1952 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://anonscm.debian.org/git/debian-med/samtools.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/samtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 4068 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main samtools 1.7-2 (dsc) [2220 B]
Get:2 http://172.17.0.1/private buster-staging/main samtools 1.7-2 (tar) [4045 kB]
Get:3 http://172.17.0.1/private buster-staging/main samtools 1.7-2 (diff) [20.4 kB]
Fetched 4068 kB in 1s (3805 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/samtools-lX0KVn/samtools-1.7' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/samtools-lX0KVn' 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-UsCrWT/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-UsCrWT/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-UsCrWT/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-UsCrWT/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UsCrWT/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UsCrWT/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UsCrWT/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-UsCrWT/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (8665 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 1 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-UsCrWT/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15677 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.7), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0)
Filtered Build-Depends: debhelper (>= 11~), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.7), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0)
dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/<<BUILDDIR>>/resolver-UsCrWT/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-UsCrWT/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UsCrWT/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UsCrWT/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UsCrWT/apt_archive ./ Sources [573 B]
Get:5 copy:/<<BUILDDIR>>/resolver-UsCrWT/apt_archive ./ Packages [649 B]
Fetched 2555 B in 0s (10.4 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install samtools build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bash-completion
bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
libcroco3 libcurl3-gnutls libfile-stripnondeterminism-perl libglib2.0-0
libgssapi-krb5-2 libhts-dev libhts2 libicu57 libio-pty-perl libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1
libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2
libssh2-1 libtimedate-perl libtinfo-dev libtool libxml2 m4 man-db pkg-config
po-debconf tabix zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz
gettext-doc libasprintf-dev libgettextpo-dev groff 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 libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bash-completion
bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
libcroco3 libcurl3-gnutls libfile-stripnondeterminism-perl libglib2.0-0
libgssapi-krb5-2 libhts-dev libhts2 libicu57 libio-pty-perl libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1
libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2
libssh2-1 libtimedate-perl libtinfo-dev libtool libxml2 m4 man-db pkg-config
po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
0 upgraded, 51 newly installed, 0 to remove and 1 not upgraded.
Need to get 12.4 MB/22.6 MB of archives.
After this operation, 79.9 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-UsCrWT/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [932 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.2-1 [1145 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf autoconf-archive all 20170928-2 [744 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf bash-completion all 1:2.7-1 [202 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-1 [32.2 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 17 [16.5 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.0-4 [2749 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.1.6 [1009 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.1-1 [51.4 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libio-pty-perl armhf 1:1.08-1.1+b3 [32.9 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libtinfo-dev armhf 6.1-1 [66.6 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1-1 [152 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf tabix armhf 1.7-2 [260 kB]
debconf: delaying package configuration, since apt-utils is not installed
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find: '/etc/bash_completion.d/': No such file or directory
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Setting up libglib2.0-0:armhf (2.56.0-4) ...
No schema files found: removed existing output file.
Setting up libtinfo-dev:armhf (6.1-1) ...
Setting up gettext-base (0.19.8.1-6) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-9) ...
Setting up libbsd0:armhf (0.8.7-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-6.1) ...
Setting up libmagic-mgc (1:5.32-2) ...
Setting up libmagic1:armhf (1:5.32-2) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libncurses5-dev:armhf (6.1-1) ...
Setting up pkg-config (0.29-4) ...
Setting up autoconf-archive (20170928-2) ...
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.27-2+rpi1) ...
Setting up autotools-dev (20180224.1) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up libkeyutils1:armhf (1.5.9-9.2) ...
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 autopoint (0.19.8.1-6) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up gettext (0.19.8.1-6) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-2) ...
Setting up libkrb5support0:armhf (1.16-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up libcurl3-gnutls:armhf (7.58.0-2) ...
Setting up tabix (1.7-2) ...
Setting up libhts2:armhf (1.7-2) ...
Setting up libhts-dev:armhf (1.7-2) ...
Setting up dh-autoreconf (17) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (11.1.6) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.30-8+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-2+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180321-1+rpi1 linux-libc-dev_4.15.11-1+rpi1
Package versions: adduser_3.117 apt_1.6~beta1 autoconf_2.69-11 autoconf-archive_20170928-2 automake_1:1.15.1-3 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.44 bash_4.4.18-1.1 bash-completion_1:2.7-1 binutils_2.30-8+rpi1 binutils-arm-linux-gnueabihf_2.30-8+rpi1 binutils-common_2.30-8+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 debconf_1.5.66 debhelper_11.1.6 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-1 e2fsprogs_1.44.1-1 e2fsprogs-l10n_1.44.1-1 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.32-2 findutils_4.6.0+git+20171230-2 g++_4:7.2.0-1d1 g++-7_7.3.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180321-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6~beta1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180321-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-8+rpi1 libblkid1_2.31.1-0.5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-2+rpi1 libc-dev-bin_2.27-2+rpi1 libc6_2.27-2+rpi1 libc6-dev_2.27-2+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180321-1+rpi1 libcilkrts5_7.3.0-12 libcom-err2_1.44.1-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.58.0-2 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libexpat1_2.2.5-3 libext2fs2_1.44.1-1 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180321-1+rpi1 libgcrypt20_1.8.1-4 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.0-4 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180321-1+rpi1 libgpg-error0_1.28-2 libgssapi-krb5-2_1.16-2 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libicu57_57.1-9 libidn11_1.33-2.1 libidn2-0_2.0.4-1.1 libio-pty-perl_1:1.08-1.1+b3 libip4tc0_1.6.2-1 libisl15_0.18-4 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1 libncurses5-dev_6.1-1 libncursesw5_6.1-1 libnettle6_3.4-1 libnghttp2-14_1.31.0-1 libnpth0_1.5-3 libnss-systemd_238-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-3 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.1-5 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-4 libpsl5_0.20.1-1 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-1 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.22.0-2 libss2_1.44.1-1 libssh2-1_1.8.0-1 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180321-1+rpi1 libsystemd0_238-3 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo-dev_6.1-1 libtinfo5_6.1-1 libtool_2.4.6-2 libubsan0_7.3.0-12 libudev1_238-3 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libxml2_2.9.4+dfsg1-6.1 linux-base_4.5 linux-libc-dev_4.15.11-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.2-1 mawk_1.3.3-17 mount_2.31.1-0.5 multiarch-support_2.27-2+rpi1 nano_2.9.4-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-1 perl_5.26.1-5 perl-base_5.26.1-5 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-5 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.12-4 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-3 systemd-sysv_238-3 sysvinit-utils_2.88dsf-59.10 tabix_1.7-2 tar_1.29b-2 tzdata_2018d-1 udev_238-3 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Mar 29 07:59:07 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./samtools_1.7-2.dsc
dpkg-source: info: extracting samtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking samtools_1.7.orig.tar.gz
dpkg-source: info: unpacking samtools_1.7-2.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying sort-tests-memory-limit.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-cc93bc07-1aad-48aa-8100-f2cc2d37b36e
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package samtools
dpkg-buildpackage: info: source version 1.7-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build samtools-1.7
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from samtools-1.7/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 -O 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*
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
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[2]: Entering directory '/<<PKGBUILDDIR>>'
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
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 --libexecdir=\${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 -O "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
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
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_cat.o bam_cat.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_md.o bam_md.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_reheader.o bam_reheader.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_plcmd.o bam_plcmd.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 sam_view.o sam_view.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 bedidx.o bedidx.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_rmdup.o bam_rmdup.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_mate.o bam_mate.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_stat.o bam_stat.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
echo '#define SAMTOOLS_VERSION "1.7"' > version.h
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_rmdupse.o bam_rmdupse.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_color.o bam_color.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 sample.o sample.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 bam2bcf.o bam2bcf.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 cut_target.o cut_target.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 bam2depth.o bam2depth.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 bam2bcf_indel.o bam2bcf_indel.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 bedcov.o bedcov.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 padding.o padding.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 faidx.o faidx.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 dict.o dict.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 bamshuf.o bamshuf.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_sort.o bam_sort.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 phase.o phase.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_flags.o bam_flags.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 stats_isize.o stats_isize.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_tview_curses.o bam_tview_curses.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_tview.o bam_tview.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_split.o bam_split.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_tview_html.o bam_tview_html.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_quickcheck.o bam_quickcheck.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_addrprg.o bam_addrprg.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_lpileup.o bam_lpileup.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 stats.o stats.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_aux.o bam_aux.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 tmp_file.o tmp_file.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_import.o bam_import.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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.o bam.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 sam.o sam.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_plbuf.o bam_plbuf.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 sam_opts.o sam_opts.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 sam_utils.o sam_utils.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_markdup.o bam_markdup.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
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
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 sam_header.o sam_header.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 misc/maq2sam-short.o misc/maq2sam.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 misc/md5sum-lite.o misc/md5sum-lite.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 misc/md5fa.o misc/md5fa.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 misc/ace2sam.o misc/ace2sam.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 test/test.o test/test.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 misc/wgsim.o misc/wgsim.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 lz4/lz4.o lz4/lz4.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 test/split/test_count_rg.o test/split/test_count_rg.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 test/split/test_expand_format_string.o test/split/test_expand_format_string.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 test/merge/test_bam_translate.o test/merge/test_bam_translate.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 test/vcf-miniview.o test/vcf-miniview.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 bamtk.o bamtk.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
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')
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
ar -rcs libst.a sam_opts.o sam_utils.o
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 test/split/test_parse_args.o test/split/test_parse_args.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lhts -lz
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -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[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o libst.a -lhts -lz -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -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
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -L./lz4 -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.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 -O 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/c6NfgcnNsc/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 979200 -s 6 /tmp/c6NfgcnNsc/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 652804 -s 6 /tmp/c6NfgcnNsc/bgzip.dat.gz
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/c6NfgcnNsc/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/c6NfgcnNsc/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/c6NfgcnNsc/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/c6NfgcnNsc/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/c6NfgcnNsc/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/c6NfgcnNsc/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/c6NfgcnNsc/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/c6NfgcnNsc/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. 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/c6NfgcnNsc/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/c6NfgcnNsc/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view /tmp/c6NfgcnNsc/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/c6NfgcnNsc/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/c6NfgcnNsc/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/c6NfgcnNsc/mpileup.bam.list -f /tmp/c6NfgcnNsc/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/c6NfgcnNsc/mpileup.cram.list -f /tmp/c6NfgcnNsc/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/c6NfgcnNsc/mpileup.bam.urllist -f /tmp/c6NfgcnNsc/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/c6NfgcnNsc/mpileup.cram.urllist -f /tmp/c6NfgcnNsc/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/c6NfgcnNsc/mpileup.bam.list -f /tmp/c6NfgcnNsc/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/c6NfgcnNsc/mpileup.cram.list -f /tmp/c6NfgcnNsc/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/c6NfgcnNsc/mpileup.cram.list -f /tmp/c6NfgcnNsc/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/c6NfgcnNsc/mpileup.cram.list -f /tmp/c6NfgcnNsc/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/c6NfgcnNsc/mpileup.ref.fa.gz -r17:1050-1060 /tmp/c6NfgcnNsc/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/c6NfgcnNsc/mpileup.ref.fa.gz -r17:1050-1060 /tmp/c6NfgcnNsc/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
samtools has subcommands: dict, faidx, 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 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
Usage on stderr rather than stdout
.. expected failure
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/c6NfgcnNsc/view.001.fogn (SAM input) .. ok
50: Count -R /tmp/c6NfgcnNsc/view.001.fogn (SAM input) .. ok
51: Filter -R /tmp/c6NfgcnNsc/view.001.fogn (BAM input) .. ok
52: Count -R /tmp/c6NfgcnNsc/view.001.fogn (BAM input) .. ok
53: Filter -R /tmp/c6NfgcnNsc/view.001.fogn (CRAM input) .. ok
54: Count -R /tmp/c6NfgcnNsc/view.001.fogn (CRAM input) .. ok
55: Filter -R /tmp/c6NfgcnNsc/view.001.fogn -r grp2 (SAM input).. ok
56: Count -R /tmp/c6NfgcnNsc/view.001.fogn -r grp2 (SAM input).. ok
57: Filter -R /tmp/c6NfgcnNsc/view.001.fogn -r grp2 (BAM input).. ok
58: Count -R /tmp/c6NfgcnNsc/view.001.fogn -r grp2 (BAM input).. ok
59: Filter -R /tmp/c6NfgcnNsc/view.001.fogn -r grp2 (CRAM input).. ok
60: Count -R /tmp/c6NfgcnNsc/view.001.fogn -r grp2 (CRAM input).. ok
61: Filter -r grp2 -R /tmp/c6NfgcnNsc/view.001.fogn (SAM input).. ok
62: Count -r grp2 -R /tmp/c6NfgcnNsc/view.001.fogn (SAM input).. ok
63: Filter -r grp2 -R /tmp/c6NfgcnNsc/view.001.fogn (BAM input).. ok
64: Count -r grp2 -R /tmp/c6NfgcnNsc/view.001.fogn (BAM input).. ok
65: Filter -r grp2 -R /tmp/c6NfgcnNsc/view.001.fogn (CRAM input).. ok
66: Count -r grp2 -R /tmp/c6NfgcnNsc/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:
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_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_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 - /<<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 - /<<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 -b /tmp/rDlbhVSYZv - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 - /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -r -s 1 - /<<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 - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 - /<<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/c6NfgcnNsc/merge.tag.1.bam /tmp/c6NfgcnNsc/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/c6NfgcnNsc/merge.tag.3.bam /tmp/c6NfgcnNsc/merge.tag.4.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 - /<<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 - /<<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 -b /tmp/Xv5MhBurZR - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 - /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -r -s 1 - /<<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 - /<<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 - /<<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/c6NfgcnNsc/merge.tag.1.bam /tmp/c6NfgcnNsc/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/c6NfgcnNsc/merge.tag.3.bam /tmp/c6NfgcnNsc/merge.tag.4.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/c6NfgcnNsc/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/c6NfgcnNsc/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/c6NfgcnNsc/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/c6NfgcnNsc/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/c6NfgcnNsc/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/c6NfgcnNsc/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_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_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.
[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.
[markdup] error: no ms score tag.
.. 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.
[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.
[markdup] error: no ms score tag.
.. 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
Number of tests:
total .. 522
passed .. 497
failed .. 0
expected failure .. 25
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 -O 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>>'
dh_install -a
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
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 ./debian/reference 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
dh_installchangelogs -a
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
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/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
man -l --recode UTF-8 ./debian/samtools/usr/share/man/man1/samtools.1 > debian/samtools/usr/share/man/man1/samtools.1.dh-new
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
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/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
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 1522310147 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.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.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 \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -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_strip -a
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1d
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1d/a65613a5da0202a0f9043cb8067e481750c8b6.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1d/a65613a5da0202a0f9043cb8067e481750c8b6.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1d/a65613a5da0202a0f9043cb8067e481750c8b6.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/1d/a65613a5da0202a0f9043cb8067e481750c8b6.debug debian/samtools/usr/bin/wgsim
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/36
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/36/da409508191dceffd3df930ed50f45e7d6d351.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/36/da409508191dceffd3df930ed50f45e7d6d351.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/36/da409508191dceffd3df930ed50f45e7d6d351.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/36/da409508191dceffd3df930ed50f45e7d6d351.debug debian/samtools/usr/bin/maq2sam-short
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7d
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7d/9bf39d8640792d488c5d70d3984cb8a70a017a.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7d/9bf39d8640792d488c5d70d3984cb8a70a017a.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7d/9bf39d8640792d488c5d70d3984cb8a70a017a.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/7d/9bf39d8640792d488c5d70d3984cb8a70a017a.debug debian/samtools/usr/bin/ace2sam
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/15
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/15/bfacb3483f4568f8c8e219a942c0e8afbadd9f.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/15/bfacb3483f4568f8c8e219a942c0e8afbadd9f.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/15/bfacb3483f4568f8c8e219a942c0e8afbadd9f.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/15/bfacb3483f4568f8c8e219a942c0e8afbadd9f.debug debian/samtools/usr/bin/maq2sam-long
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1b
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1b/9583ecfe2a37cb0ac4e0bedb187225f4f6ca16.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1b/9583ecfe2a37cb0ac4e0bedb187225f4f6ca16.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1b/9583ecfe2a37cb0ac4e0bedb187225f4f6ca16.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/1b/9583ecfe2a37cb0ac4e0bedb187225f4f6ca16.debug debian/samtools/usr/bin/samtools
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c1
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c1/f374962830816d77438b3076f00fbe496121eb.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c1/f374962830816d77438b3076f00fbe496121eb.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c1/f374962830816d77438b3076f00fbe496121eb.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/c1/f374962830816d77438b3076f00fbe496121eb.debug debian/samtools/usr/bin/md5fa
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5a
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5a/0d23ace7e62b42f681c430781e520df8ae4bfa.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5a/0d23ace7e62b42f681c430781e520df8ae4bfa.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5a/0d23ace7e62b42f681c430781e520df8ae4bfa.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5a/0d23ace7e62b42f681c430781e520df8ae4bfa.debug debian/samtools/usr/bin/md5sum-lite
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/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite 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=15bfacb3483f4568f8c8e219a942c0e8afbadd9f 1b9583ecfe2a37cb0ac4e0bedb187225f4f6ca16 1da65613a5da0202a0f9043cb8067e481750c8b6 36da409508191dceffd3df930ed50f45e7d6d351 5a0d23ace7e62b42f681c430781e520df8ae4bfa 7d9bf39d8640792d488c5d70d3984cb8a70a017a c1f374962830816d77438b3076f00fbe496121eb" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
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: unused substitution variable ${perl:Depends}
chmod 0644 -- debian/samtools/DEBIAN/control
chown 0:0 -- debian/samtools/DEBIAN/control
dh_md5sums -a
(cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
chmod 0644 -- debian/samtools/DEBIAN/md5sums
chown 0:0 -- debian/samtools/DEBIAN/md5sums
(cd debian/.debhelper/samtools/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --build debian/samtools ..
dpkg-deb --build debian/.debhelper/samtools/dbgsym-root ..
dpkg-deb: building package 'samtools' in '../samtools_1.7-2_armhf.deb'.
dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.7-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../samtools_1.7-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.7
dpkg-source: info: using options from samtools-1.7/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-04-04T06:39:21Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
samtools_1.7-2_armhf.changes:
-----------------------------
Format: 1.8
Date: Thu, 29 Mar 2018 09:55:47 +0200
Source: samtools
Binary: samtools samtools-test
Architecture: armhf
Version: 1.7-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
samtools-test - test files for the samtools package
Changes:
samtools (1.7-2) unstable; urgency=medium
.
* Install examples (since it is used in dwgsim package and might be
helpful for users in general)
* debhelper 11
Checksums-Sha1:
e1e3e93220d1878f6c0f8fe8483a49ce93476e39 577768 samtools-dbgsym_1.7-2_armhf.deb
492d18537e7d0ce59f3a5e4a12fb656b988d0f3a 5372 samtools_1.7-2_armhf.buildinfo
cdf44f8ce47cea0cf9421f4d58ee525ed7ff4341 365244 samtools_1.7-2_armhf.deb
Checksums-Sha256:
03221b8b361e7315ef5cf5a5a504e6d487092de2e4a5f961c98b6fcf82641aa5 577768 samtools-dbgsym_1.7-2_armhf.deb
45b09d51669852e57de79842c501c45ebb69609206091355ebab0d42c1c54bf6 5372 samtools_1.7-2_armhf.buildinfo
623dead57ecbae450d6b563dd1ba69bbc6e739f783bd8215190d53c40ac94106 365244 samtools_1.7-2_armhf.deb
Files:
907cb12f62d7433d4aea8efc50a55f50 577768 debug optional samtools-dbgsym_1.7-2_armhf.deb
a53829893ba524594764b2edc01165b3 5372 science optional samtools_1.7-2_armhf.buildinfo
c0ce33ba91149ca47906761867ede4cc 365244 science optional samtools_1.7-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
samtools-dbgsym_1.7-2_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 577768 bytes: control archive=852 bytes.
616 bytes, 12 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
Version: 1.7-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 648
Depends: samtools (= 1.7-2)
Section: debug
Priority: optional
Description: debug symbols for samtools
Build-Ids: 15bfacb3483f4568f8c8e219a942c0e8afbadd9f 1b9583ecfe2a37cb0ac4e0bedb187225f4f6ca16 1da65613a5da0202a0f9043cb8067e481750c8b6 36da409508191dceffd3df930ed50f45e7d6d351 5a0d23ace7e62b42f681c430781e520df8ae4bfa 7d9bf39d8640792d488c5d70d3984cb8a70a017a c1f374962830816d77438b3076f00fbe496121eb
drwxr-xr-x root/root 0 2018-03-29 07:55 ./
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/lib/
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/lib/debug/.build-id/15/
-rw-r--r-- root/root 11224 2018-03-29 07:55 ./usr/lib/debug/.build-id/15/bfacb3483f4568f8c8e219a942c0e8afbadd9f.debug
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/lib/debug/.build-id/1b/
-rw-r--r-- root/root 563928 2018-03-29 07:55 ./usr/lib/debug/.build-id/1b/9583ecfe2a37cb0ac4e0bedb187225f4f6ca16.debug
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/lib/debug/.build-id/1d/
-rw-r--r-- root/root 19436 2018-03-29 07:55 ./usr/lib/debug/.build-id/1d/a65613a5da0202a0f9043cb8067e481750c8b6.debug
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/lib/debug/.build-id/36/
-rw-r--r-- root/root 11224 2018-03-29 07:55 ./usr/lib/debug/.build-id/36/da409508191dceffd3df930ed50f45e7d6d351.debug
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/lib/debug/.build-id/5a/
-rw-r--r-- root/root 8348 2018-03-29 07:55 ./usr/lib/debug/.build-id/5a/0d23ace7e62b42f681c430781e520df8ae4bfa.debug
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/lib/debug/.build-id/7d/
-rw-r--r-- root/root 19732 2018-03-29 07:55 ./usr/lib/debug/.build-id/7d/9bf39d8640792d488c5d70d3984cb8a70a017a.debug
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/lib/debug/.build-id/c1/
-rw-r--r-- root/root 10988 2018-03-29 07:55 ./usr/lib/debug/.build-id/c1/f374962830816d77438b3076f00fbe496121eb.debug
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/share/
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-03-29 07:55 ./usr/share/doc/samtools-dbgsym -> samtools
samtools_1.7-2_armhf.deb
------------------------
new Debian package, version 2.0.
size 365244 bytes: control archive=1948 bytes.
815 bytes, 17 lines control
2634 bytes, 42 lines md5sums
Package: samtools
Version: 1.7-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 838
Depends: libc6 (>= 2.7), libhts2 (>= 1.7), libncurses5 (>= 6), libtinfo5 (>= 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 and BAM 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) format, 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 (not SAM) file on a remote FTP or HTTP
server.
drwxr-xr-x root/root 0 2018-03-29 07:55 ./
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/bin/
-rwxr-xr-x root/root 17988 2018-03-29 07:55 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5333 2018-01-26 12:11 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2018-01-26 12:11 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2018-01-26 12:11 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2018-01-26 12:11 ./usr/bin/interpolate_sam.pl
-rwxr-xr-x root/root 9784 2018-03-29 07:55 ./usr/bin/maq2sam-long
-rwxr-xr-x root/root 9784 2018-03-29 07:55 ./usr/bin/maq2sam-short
-rwxr-xr-x root/root 9800 2018-03-29 07:55 ./usr/bin/md5fa
-rwxr-xr-x root/root 5668 2018-03-29 07:55 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2018-01-26 12:11 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48659 2018-01-26 12:11 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2018-01-26 12:11 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2018-01-26 12:11 ./usr/bin/sam2vcf.pl
-rwxr-xr-x root/root 428660 2018-03-29 07:55 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2018-01-26 12:11 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2018-01-26 12:11 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2018-01-26 12:11 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2018-01-26 12:11 ./usr/bin/varfilter.py
-rwxr-xr-x root/root 18052 2018-03-29 07:55 ./usr/bin/wgsim
-rwxr-xr-x root/root 12540 2018-01-26 12:11 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2018-01-26 12:11 ./usr/bin/zoom2sam.pl
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/share/
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/share/commonwl/
-rwxr-xr-x root/root 1906 2018-03-29 07:55 ./usr/share/commonwl/samtools-faidx.cwl
-rwxr-xr-x root/root 1979 2018-03-29 07:55 ./usr/share/commonwl/samtools-index.cwl
-rwxr-xr-x root/root 1627 2018-03-29 07:55 ./usr/share/commonwl/samtools-rmdup.cwl
-rwxr-xr-x root/root 2834 2018-03-29 07:55 ./usr/share/commonwl/samtools-sort.cwl
-rwxr-xr-x root/root 6224 2018-03-29 07:55 ./usr/share/commonwl/samtools-view.cwl
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2018-01-26 12:11 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 295 2018-03-29 07:55 ./usr/share/doc/samtools/NEWS.Debian.gz
-rw-r--r-- root/root 721 2018-03-29 07:55 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 4711 2018-03-29 07:55 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 3451 2018-03-29 07:55 ./usr/share/doc/samtools/copyright
drwxr-xr-x root/root 0 2018-03-29 07:55 ./usr/share/doc/samtools/examples/
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 19216
Build-Time: 188
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 158
Job: samtools_1.7-2
Machine Architecture: armhf
Package: samtools
Package-Time: 365
Source-Version: 1.7-2
Space: 19216
Status: successful
Version: 1.7-2
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Finished at 2018-04-04T06:39:21Z
Build needed 00:06:05, 19216k disk space