samtools →
1.19.2-1 →
armhf → 2024-02-20 06:08:24
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| samtools 1.19.2-1 (armhf) Tue, 20 Feb 2024 05:55:25 +0000 |
+==============================================================================+
Package: samtools
Version: 1.19.2-1
Source Version: 1.19.2-1
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-8d7f6eed-bcb5-4d90-8d37-df6710051fb3' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/samtools-L6Geqi/resolver-tXfDil' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.5 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.1 MB]
Fetched 29.6 MB in 11s (2713 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/samtools.git
Please use:
git clone https://salsa.debian.org/med-team/samtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 5690 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main samtools 1.19.2-1 (dsc) [2295 B]
Get:2 http://172.17.4.1/private trixie-staging/main samtools 1.19.2-1 (tar) [5666 kB]
Get:3 http://172.17.4.1/private trixie-staging/main samtools 1.19.2-1 (diff) [21.8 kB]
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I: NOTICE: Log filtering will replace 'build/samtools-L6Geqi/samtools-1.19.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/samtools-L6Geqi' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
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Reading package lists...
Reading package lists...
Install main 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:
krb5-locales libpam-cap util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bash-completion
bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file
gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl
libhts-dev libhts3 libhtscodecs2 libicu72 libio-pty-perl liblzma-dev
libmagic-mgc libmagic1 libncurses-dev libncurses6 libnghttp2-14 libpipeline1
libpkgconf3 libpsl5 librtmp1 libssh2-1 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db pkgconf pkgconf-bin po-debconf tabix
zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev
libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev
libldap2-dev librtmp-dev libssh2-1-dev liblzma-doc ncurses-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl libgpm2
publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bash-completion
bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file
gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl
libhts-dev libhts3 libhtscodecs2 libicu72 libio-pty-perl liblzma-dev
libmagic-mgc libmagic1 libncurses-dev libncurses6 libnghttp2-14 libpipeline1
libpkgconf3 libpsl5 librtmp1 libssh2-1 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db pkgconf pkgconf-bin po-debconf
sbuild-build-depends-main-dummy tabix zlib1g-dev
0 upgraded, 54 newly installed, 0 to remove and 29 not upgraded.
Need to get 24.7 MB of archives.
After this operation, 94.4 MB of additional disk space will be used.
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Get:2 http://172.17.4.1/private trixie-staging/main armhf autoconf-archive all 20220903-3 [775 kB]
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Get:17 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
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Get:28 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
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Get:36 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-4 [195 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.5.0-2+rpi1 [372 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libcurl4-gnutls-dev armhf 8.5.0-2+rpi1 [456 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.19-1 [39.0 kB]
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Get:44 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.18+ds-1 [380 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf liblzma-dev armhf 5.4.5-0.3 [278 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.3.dfsg-3 [903 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libhts-dev armhf 1.18+ds-1 [1539 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libio-pty-perl armhf 1:1.20-1 [33.7 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libncurses6 armhf 6.4+20240113-1 [80.9 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libncurses-dev armhf 6.4+20240113-1 [289 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf pkgconf-bin armhf 1.8.1-1 [27.8 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf pkgconf armhf 1.8.1-1 [25.9 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf tabix armhf 1.18+ds-1 [380 kB]
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Setting up libhtscodecs2:armhf (1.6.0-1) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up libpsl5:armhf (0.21.2-1+b1) ...
Setting up libicu72:armhf (72.1-4) ...
Setting up bsdextrautils (2.39.3-6) ...
Setting up libio-pty-perl (1:1.20-1) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.13) ...
Setting up libbrotli1:armhf (1.1.0-2) ...
Setting up libnghttp2-14:armhf (1.59.0-1) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up libdeflate0:armhf (1.19-1) ...
Setting up gettext-base (0.21-14) ...
Setting up m4 (1.4.19-4) ...
Setting up autoconf-archive (20220903-3) ...
Setting up file (1:5.45-2) ...
Setting up autotools-dev (20220109.1) ...
Setting up libpkgconf3:armhf (1.8.1-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up bash-completion (1:2.11-8) ...
Setting up libncurses6:armhf (6.4+20240113-1) ...
Setting up autopoint (0.21-14) ...
Setting up pkgconf-bin (1.8.1-1) ...
Setting up autoconf (2.71-3) ...
Setting up liblzma-dev:armhf (5.4.5-0.3) ...
Setting up zlib1g-dev:armhf (1:1.3.dfsg-3) ...
Setting up libuchardet0:armhf (0.0.8-1) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libssh2-1:armhf (1.11.0-4) ...
Setting up libdeflate-dev:armhf (1.19-1) ...
Setting up tabix (1.18+ds-1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up libbz2-dev:armhf (1.0.8-5+b2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libncurses-dev:armhf (6.4+20240113-1) ...
Setting up gettext (0.21-14) ...
Setting up libtool (2.4.7-7) ...
Setting up libcurl3-gnutls:armhf (8.5.0-2+rpi1) ...
Setting up libcurl4-gnutls-dev:armhf (8.5.0-2+rpi1) ...
Setting up pkgconf:armhf (1.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up libhts3:armhf (1.18+ds-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.18+ds-1) ...
Setting up man-db (2.12.0-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.13) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-13+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.2+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 libc6-dev_2.37-13+rpi1 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 linux-libc-dev_6.5.6-1+rpi1+b1
Package versions: adduser_3.137 apt_2.7.9 autoconf_2.71-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 bash-completion_1:2.11-8 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.4-3 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-9+rpi1 dash_0.5.12-6 debconf_1.5.83 debhelper_13.13 debianutils_5.16 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.2+rpi1 dpkg-dev_1.22.2+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc_4:13.2.0-1+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 gcc-13-base_13.2.0-9+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-5 libacl1_2.3.1-6 libapt-pkg6.0_2.7.9 libarchive-zip-perl_1.68-1 libasan8_13.2.0-9+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-9+rpi1 libattr1_1:2.5.1-5 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.3-6 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.37-13+rpi1 libc-dev-bin_2.37-13+rpi1 libc6_2.37-13+rpi1 libc6-dev_2.37-13+rpi1 libcap-ng0_0.8.4-1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_13.2.0-9+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcurl3-gnutls_8.5.0-2+rpi1 libcurl4-gnutls-dev_8.5.0-2+rpi1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.13 libdeflate-dev_1.19-1 libdeflate0_1.19-1 libdpkg-perl_1.22.2+rpi1 libelf1_0.188-2.1+rpi1 libext2fs2_1.47.0-2 libfakeroot_1.33-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-13+rpi1 libgcc-13-dev_13.2.0-9+rpi1 libgcc-s1_13.2.0-9+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.3-1 libgomp1_13.2.0-9+rpi1 libgpg-error0_1.47-3 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libhts-dev_1.18+ds-1 libhts3_1.18+ds-1 libhtscodecs2_1.6.0-1 libicu72_72.1-4 libidn2-0_2.3.4-1 libio-pty-perl_1:1.20-1 libisl23_0.26-3 libjansson4_2.14-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1+b1 liblz4-1_1.9.4-1+rpi1+b1 liblzma-dev_5.4.5-0.3 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-2 libmount1_2.39.3-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncurses-dev_6.4+20240113-1 libncurses6_6.4+20240113-1 libncursesw6_6.4+20240113-1 libnettle8_3.9.1-2 libnghttp2-14_1.59.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-4 libpam-cap_1:2.66-4 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-1 libpsl5_0.21.2-1+b1 libreadline8_8.2-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2+rpi1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol1_3.1-1 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.3-6 libsqlite3-0_3.44.2-1 libss2_1.47.0-2 libssh2-1_1.11.0-4 libssl1.1_1.1.1o-1 libssl3_3.1.4-2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtinfo6_6.4+20240113-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-9+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-6 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1+b1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-3 mawk_1.3.4.20231126-1 mount_2.39.3-6 nano_7.2-2 ncurses-base_6.4+20240113-1 ncurses-bin_6.4+20240113-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3 pkgconf_1.8.1-1 pkgconf-bin_1.8.1-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.20 sysvinit-utils_3.08-5 tabix_1.18+ds-1 tar_1.35+dfsg-3 tzdata_2023d-1 usrmerge_39 util-linux_2.39.3-6 util-linux-extra_2.39.3-6 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3 zlib1g-dev_1:1.3.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: samtools
Binary: samtools, samtools-test
Architecture: any all
Version: 1.19.2-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://www.htslib.org/
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/samtools
Vcs-Git: https://salsa.debian.org/med-team/samtools.git
Testsuite: autopkgtest
Testsuite-Triggers: tabix
Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl <!nocheck>, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev
Package-List:
samtools deb science optional arch=any
samtools-test deb science optional arch=all
Checksums-Sha1:
8dff98a03e9295730b24e26cb1447b41887af669 5666279 samtools_1.19.2.orig.tar.gz
ac8048d48e8883df9b4700dd4a26bccd6542cfc8 21752 samtools_1.19.2-1.debian.tar.xz
Checksums-Sha256:
93b4ee042003d536a2f822a17dd5e65439f724214d5d2b5becc8a9f190ef2efd 5666279 samtools_1.19.2.orig.tar.gz
ab11a07d6e8e80fadb62672ec5974867a0328f31d5b6faa7c2d8e5b7de9936a1 21752 samtools_1.19.2-1.debian.tar.xz
Files:
dc7d1649a27689287499876dc05785c4 5666279 samtools_1.19.2.orig.tar.gz
3eea35b7ce97c48454c4f5b378ab722a 21752 samtools_1.19.2-1.debian.tar.xz
-----BEGIN PGP SIGNATURE-----
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-----END PGP SIGNATURE-----
gpgv: Signature made Sat Feb 17 17:32:01 2024 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./samtools_1.19.2-1.dsc: no acceptable signature found
dpkg-source: info: extracting samtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking samtools_1.19.2.orig.tar.gz
dpkg-source: info: unpacking samtools_1.19.2-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying reproducible.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=539dea8b567c411499a729ba3d4ba4c9
JOURNAL_STREAM=8:41227
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-8d7f6eed-bcb5-4d90-8d37-df6710051fb3
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c35660
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package samtools
dpkg-buildpackage: info: source version 1.19.2-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from samtools-1.19.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f config.mk
touch config.mk
dh_auto_clean --
make -j4 distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd test/dat && rm -f test_input_*.bam.bai view.*.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*
cd test/reference && rm -f mpileup.*.fai
rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o
rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
rm -rf autom4te.cache
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files
rm -fr -- debian/samtools/ debian/tmp/ debian/samtools-test/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p
" > debian/autoreconf.before
grep -q ^XDT_ configure.ac
autoreconf -f -i
configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals
./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p
" > debian/autoreconf.after
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
touch config.mk
aclocal --force -I debian/ -I /usr/share/aclocal
autoconf
configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals
./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
dh_auto_configure -- --with-htslib=system
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
checking for gawk... no
checking for mawk... mawk
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for Curses library... yes
checking for working curses.h... yes
checking for X/Open Enhanced Curses conformance... no
checking for Curses color functions... yes
checking for obsolete Curses functions... yes
checking for library containing cbreak... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/samtools.debhelper.log
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
make -j4 "CFLAGS=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
echo '#define SAMTOOLS_VERSION "1.19.2"' > version.h
echo '#define SAMTOOLS_CC "gcc"' >> version.h
echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h
echo '#define SAMTOOLS_CFLAGS "-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security"' >> version.h
echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h
echo '#define SAMTOOLS_HTSDIR ""' >> version.h
echo '#define SAMTOOLS_LIBS ""' >> version.h
echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram_size.o cram_size.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz
gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/samtools.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -- BGZIP=/usr/bin/bgzip
make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/<<PKGBUILDDIR>>'
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
test/split/test_parse_args
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-}
test_reference:
/<<PKGBUILDDIR>>/samtools reference test/reference/mpileup.1.tmp.cram
.. ok
test_reference:
/<<PKGBUILDDIR>>/samtools reference -e test/reference/mpileup.1.tmp.cram
.. ok
test_reference:
/<<PKGBUILDDIR>>/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
.. ok
test_reference:
/<<PKGBUILDDIR>>/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
.. ok
test_reference:
/<<PKGBUILDDIR>>/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram
.. ok
test_reference:
/<<PKGBUILDDIR>>/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram
.. ok
test_reference:
/<<PKGBUILDDIR>>/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
.. ok
test_reference:
/<<PKGBUILDDIR>>/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
.. ok
/usr/bin/bgzip -c -b 65272 -s 5 /tmp/mx6BYkc173/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 979200 -s 6 /tmp/mx6BYkc173/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 652804 -s 6 /tmp/mx6BYkc173/bgzip.dat.gz
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/mx6BYkc173/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/mx6BYkc173/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/mx6BYkc173/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/mx6BYkc173/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/mx6BYkc173/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/mx6BYkc173/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/mx6BYkc173/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/mx6BYkc173/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/mx6BYkc173/fqidx.fq 3:11-13
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/mx6BYkc173/fqidx.fq.gz 3:11-13
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/mx6BYkc173/fqidx.fq 2:998-1003
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/mx6BYkc173/fqidx.fq.gz 2:998-1003
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/mx6BYkc173/fqidx.fq 1:100-104
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/mx6BYkc173/fqidx.fq.gz 1:100-104
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/mx6BYkc173/fqidx.fq 1:99998-100007
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/mx6BYkc173/fqidx.fq.gz 1:99998-100007
.. ok
.. ok
test_dict:
/<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /<<PKGBUILDDIR>>/test/dat/dict.fa
.. ok
test_dict:
/<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/mx6BYkc173/dict.fa.gz
.. ok
test_dict:
cat /<<PKGBUILDDIR>>/test/dat/dict.fa | /<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz
.. ok
test_dict:
/<<PKGBUILDDIR>>/samtools dict -AH < /<<PKGBUILDDIR>>/test/dat/dict.alias.fa
.. ok
test_dict:
/<<PKGBUILDDIR>>/samtools dict -H -l /<<PKGBUILDDIR>>/test/dat/dict.alt < /<<PKGBUILDDIR>>/test/dat/dict.alias.fa
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view /tmp/mx6BYkc173/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view /tmp/mx6BYkc173/large_chrom.bam ref2:1-541556283
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam && cat /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/mx6BYkc173/test_input_1_b.bam.bai ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/mx6BYkc173/test_input_1_b.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools merge -O sam - -X -cp -R ref2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai /tmp/mx6BYkc173/test_input_1_b.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/mx6BYkc173/test_input_1_b_opt.bam.bai ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam && cat /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam.bai ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam /tmp/mx6BYkc173/auto_indexed.csi && cat /tmp/mx6BYkc173/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.cram /tmp/mx6BYkc173/auto_indexed.crai && cat /tmp/mx6BYkc173/auto_indexed.crai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.sam /tmp/mx6BYkc173/auto_indexed.csi && cat /tmp/mx6BYkc173/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/mx6BYkc173/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/mx6BYkc173/large_chrom.bam ref2:1-541556283
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam && cat /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/mx6BYkc173/test_input_1_b.bam.bai ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/mx6BYkc173/test_input_1_b.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -O sam - -X -cp -R ref2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai /tmp/mx6BYkc173/test_input_1_b.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/mx6BYkc173/test_input_1_b_opt.bam.bai ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 -M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam && cat /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam.bai ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam /tmp/mx6BYkc173/auto_indexed.csi && cat /tmp/mx6BYkc173/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.cram /tmp/mx6BYkc173/auto_indexed.crai && cat /tmp/mx6BYkc173/auto_indexed.crai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.sam /tmp/mx6BYkc173/auto_indexed.csi && cat /tmp/mx6BYkc173/auto_indexed.csi
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/mx6BYkc173/mpileup.bam.list -f /tmp/mx6BYkc173/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/mx6BYkc173/mpileup.cram.list -f /tmp/mx6BYkc173/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/mx6BYkc173/mpileup.bam.urllist -f /tmp/mx6BYkc173/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/mx6BYkc173/mpileup.cram.urllist -f /tmp/mx6BYkc173/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/mx6BYkc173/mpileup.ref.fa.gz -r17:1050-1060 /tmp/mx6BYkc173/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/mx6BYkc173/mpileup.ref.fa.gz -r17:1050-1060 /tmp/mx6BYkc173/mpileup.1.cram | grep -v mpileup
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup /<<PKGBUILDDIR>>/test/mpileup/overlap.bam | grep 128814202
.. ok
test_usage:
samtools
samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, reset, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, head, tview, view, depad, samples, help, version
.. ok
test_usage_subcommand:
samtools dict
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools faidx
.. ok
test_usage_subcommand:
samtools fqidx
.. ok
test_usage_subcommand:
samtools index
.. ok
test_usage_subcommand:
samtools calmd
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools fixmate
.. ok
test_usage_subcommand:
samtools reheader
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools targetcut
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools addreplacerg
.. ok
test_usage_subcommand:
samtools markdup
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools ampliconclip
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools collate
.. ok
test_usage_subcommand:
samtools cat
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools consensus
.. ok
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 import
.. ok
test_usage_subcommand:
samtools reference
.. ok
test_usage_subcommand:
samtools reset
.. ok
test_usage_subcommand:
samtools bedcov
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools coverage
.. ok
test_usage_subcommand:
samtools depth
.. ok
test_usage_subcommand:
samtools flagstat
.. ok
test_usage_subcommand:
samtools idxstats
.. ok
test_usage_subcommand:
samtools phase
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools stats
.. ok
test_usage_subcommand:
samtools ampliconstats
.. ok
test_usage_subcommand:
samtools flags
.. ok
test_usage_subcommand:
samtools head
.. ok
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_usage_subcommand:
samtools samples
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/mx6BYkc173/view.001.fogn (SAM input) .. ok
50: Count -R /tmp/mx6BYkc173/view.001.fogn (SAM input) .. ok
51: Filter -R /tmp/mx6BYkc173/view.001.fogn (BAM input) .. ok
52: Count -R /tmp/mx6BYkc173/view.001.fogn (BAM input) .. ok
53: Filter -R /tmp/mx6BYkc173/view.001.fogn (CRAM input) .. ok
54: Count -R /tmp/mx6BYkc173/view.001.fogn (CRAM input) .. ok
55: Filter -R /tmp/mx6BYkc173/view.001.fogn -r grp2 (SAM input).. ok
56: Count -R /tmp/mx6BYkc173/view.001.fogn -r grp2 (SAM input).. ok
57: Filter -R /tmp/mx6BYkc173/view.001.fogn -r grp2 (BAM input).. ok
58: Count -R /tmp/mx6BYkc173/view.001.fogn -r grp2 (BAM input).. ok
59: Filter -R /tmp/mx6BYkc173/view.001.fogn -r grp2 (CRAM input).. ok
60: Count -R /tmp/mx6BYkc173/view.001.fogn -r grp2 (CRAM input).. ok
61: Filter -r grp2 -R /tmp/mx6BYkc173/view.001.fogn (SAM input).. ok
62: Count -r grp2 -R /tmp/mx6BYkc173/view.001.fogn (SAM input).. ok
63: Filter -r grp2 -R /tmp/mx6BYkc173/view.001.fogn (BAM input).. ok
64: Count -r grp2 -R /tmp/mx6BYkc173/view.001.fogn (BAM input).. ok
65: Filter -r grp2 -R /tmp/mx6BYkc173/view.001.fogn (CRAM input).. ok
66: Count -r grp2 -R /tmp/mx6BYkc173/view.001.fogn (CRAM input).. ok
67: Filter -N /tmp/mx6BYkc173/view.001.forn (SAM input) .. ok
68: Count -N /tmp/mx6BYkc173/view.001.forn (SAM input) .. ok
69: Filter -N /tmp/mx6BYkc173/view.001.forn (BAM input) .. ok
70: Count -N /tmp/mx6BYkc173/view.001.forn (BAM input) .. ok
71: Filter -N /tmp/mx6BYkc173/view.001.forn (CRAM input) .. ok
72: Count -N /tmp/mx6BYkc173/view.001.forn (CRAM input) .. ok
73: Filter -d BC (SAM input) .. ok
74: Count -d BC (SAM input) .. ok
75: Filter -d BC (BAM input) .. ok
76: Count -d BC (BAM input) .. ok
77: Filter -d BC (CRAM input) .. ok
78: Count -d BC (CRAM input) .. ok
79: Filter -d BC:TGCA (SAM input) .. ok
80: Count -d BC:TGCA (SAM input) .. ok
81: Filter -d BC:TGCA (BAM input) .. ok
82: Count -d BC:TGCA (BAM input) .. ok
83: Filter -d BC:TGCA (CRAM input) .. ok
84: Count -d BC:TGCA (CRAM input) .. ok
85: Filter -D BC:/tmp/mx6BYkc173/view.001.fobc (SAM input) .. ok
86: Count -D BC:/tmp/mx6BYkc173/view.001.fobc (SAM input) .. ok
87: Filter -D BC:/tmp/mx6BYkc173/view.001.fobc (BAM input) .. ok
88: Count -D BC:/tmp/mx6BYkc173/view.001.fobc (BAM input) .. ok
89: Filter -D BC:/tmp/mx6BYkc173/view.001.fobc (CRAM input) .. ok
90: Count -D BC:/tmp/mx6BYkc173/view.001.fobc (CRAM input) .. ok
91: Filter -D BC:/tmp/mx6BYkc173/view.001.fobc -d BC:TGCA (SAM input).. ok
92: Count -D BC:/tmp/mx6BYkc173/view.001.fobc -d BC:TGCA (SAM input).. ok
93: Filter -D BC:/tmp/mx6BYkc173/view.001.fobc -d BC:TGCA (BAM input).. ok
94: Count -D BC:/tmp/mx6BYkc173/view.001.fobc -d BC:TGCA (BAM input).. ok
95: Filter -D BC:/tmp/mx6BYkc173/view.001.fobc -d BC:TGCA (CRAM input).. ok
96: Count -D BC:/tmp/mx6BYkc173/view.001.fobc -d BC:TGCA (CRAM input).. ok
97: Filter -d BC:TGCA -D BC:/tmp/mx6BYkc173/view.001.fobc (SAM input).. ok
98: Count -d BC:TGCA -D BC:/tmp/mx6BYkc173/view.001.fobc (SAM input).. ok
99: Filter -d BC:TGCA -D BC:/tmp/mx6BYkc173/view.001.fobc (BAM input).. ok
100: Count -d BC:TGCA -D BC:/tmp/mx6BYkc173/view.001.fobc (BAM input).. ok
101: Filter -d BC:TGCA -D BC:/tmp/mx6BYkc173/view.001.fobc (CRAM input).. ok
102: Count -d BC:TGCA -D BC:/tmp/mx6BYkc173/view.001.fobc (CRAM input).. ok
103: Filter -D RG:/tmp/mx6BYkc173/view.001.fogn (SAM input) .. ok
104: Count -D RG:/tmp/mx6BYkc173/view.001.fogn (SAM input) .. ok
105: Filter -D RG:/tmp/mx6BYkc173/view.001.fogn (BAM input) .. ok
106: Count -D RG:/tmp/mx6BYkc173/view.001.fogn (BAM input) .. ok
107: Filter -D RG:/tmp/mx6BYkc173/view.001.fogn (CRAM input).. ok
108: Count -D RG:/tmp/mx6BYkc173/view.001.fogn (CRAM input) .. ok
109: Filter -d NE:TGCA (SAM input) .. ok
110: Count -d NE:TGCA (SAM input) .. ok
111: Filter -d NE:TGCA (BAM input) .. ok
112: Count -d NE:TGCA (BAM input) .. ok
113: Filter -d NE:TGCA (CRAM input) .. ok
114: Count -d NE:TGCA (CRAM input) .. ok
115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/mx6BYkc173/view.test115.sam -h -d TGCA /tmp/mx6BYkc173/view.001.sam --no-PG
.. expected failure
116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d TGCA /tmp/mx6BYkc173/view.001.sam --no-PG
.. expected failure
117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/mx6BYkc173/view.test117.sam -h -d TGCA /tmp/mx6BYkc173/view.test001.bam --no-PG
.. expected failure
118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d TGCA /tmp/mx6BYkc173/view.test001.bam --no-PG
.. expected failure
119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/mx6BYkc173/view.test119.sam -h -d TGCA /tmp/mx6BYkc173/view.test006.cram --no-PG
.. expected failure
120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d TGCA /tmp/mx6BYkc173/view.test006.cram --no-PG
.. expected failure
121: Filter -D BClong:/tmp/mx6BYkc173/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mx6BYkc173/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/mx6BYkc173/view.test121.sam -h -D BClong:/tmp/mx6BYkc173/view.001.fobc /tmp/mx6BYkc173/view.001.sam --no-PG
.. expected failure
122: Count -D BClong:/tmp/mx6BYkc173/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mx6BYkc173/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/mx6BYkc173/view.001.fobc /tmp/mx6BYkc173/view.001.sam --no-PG
.. expected failure
123: Filter -D BClong:/tmp/mx6BYkc173/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mx6BYkc173/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/mx6BYkc173/view.test123.sam -h -D BClong:/tmp/mx6BYkc173/view.001.fobc /tmp/mx6BYkc173/view.test001.bam --no-PG
.. expected failure
124: Count -D BClong:/tmp/mx6BYkc173/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mx6BYkc173/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/mx6BYkc173/view.001.fobc /tmp/mx6BYkc173/view.test001.bam --no-PG
.. expected failure
125: Filter -D BClong:/tmp/mx6BYkc173/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mx6BYkc173/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/mx6BYkc173/view.test125.sam -h -D BClong:/tmp/mx6BYkc173/view.001.fobc /tmp/mx6BYkc173/view.test006.cram --no-PG
.. expected failure
126: Count -D BClong:/tmp/mx6BYkc173/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mx6BYkc173/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/mx6BYkc173/view.001.fobc /tmp/mx6BYkc173/view.test006.cram --no-PG
.. expected failure
127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/mx6BYkc173/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/mx6BYkc173/view.001.sam --no-PG
.. expected failure
128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/mx6BYkc173/view.001.sam --no-PG
.. expected failure
129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/mx6BYkc173/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/mx6BYkc173/view.test001.bam --no-PG
.. expected failure
130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/mx6BYkc173/view.test001.bam --no-PG
.. expected failure
131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/mx6BYkc173/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/mx6BYkc173/view.test006.cram --no-PG
.. expected failure
132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/mx6BYkc173/view.test006.cram --no-PG
.. expected failure
133: Filter -d NM:13 (SAM input) .. ok
134: Count -d NM:13 (SAM input) .. ok
135: Filter -d NM:13 (BAM input) .. ok
136: Count -d NM:13 (BAM input) .. ok
137: Filter -d NM:13 (CRAM input) .. ok
138: Count -d NM:13 (CRAM input) .. ok
139: Filter -d ab:z (SAM input) .. ok
140: Count -d ab:z (SAM input) .. ok
141: Filter -d ab:z (BAM input) .. ok
142: Count -d ab:z (BAM input) .. ok
143: Filter -d ab:z (CRAM input) .. ok
144: Count -d ab:z (CRAM input) .. ok
145: Filter -l Library 2 (SAM input) .. ok
146: Count -l Library 2 (SAM input) .. ok
147: Filter -l Library 2 (BAM input) .. ok
148: Count -l Library 2 (BAM input) .. ok
149: Filter -l Library 2 (CRAM input) .. ok
150: Count -l Library 2 (CRAM input) .. ok
151: Filter -l Library 3 (SAM input) .. ok
152: Count -l Library 3 (SAM input) .. ok
153: Filter -l Library 3 (BAM input) .. ok
154: Count -l Library 3 (BAM input) .. ok
155: Filter -l Library 3 (CRAM input) .. ok
156: Count -l Library 3 (CRAM input) .. ok
157: Filter -q 50 (SAM input) .. ok
158: Count -q 50 (SAM input) .. ok
159: Filter -q 50 (BAM input) .. ok
160: Count -q 50 (BAM input) .. ok
161: Filter -q 50 (CRAM input) .. ok
162: Count -q 50 (CRAM input) .. ok
163: Filter -q 99 (SAM input) .. ok
164: Count -q 99 (SAM input) .. ok
165: Filter -q 99 (BAM input) .. ok
166: Count -q 99 (BAM input) .. ok
167: Filter -q 99 (CRAM input) .. ok
168: Count -q 99 (CRAM input) .. ok
169: Filter -q 100 (SAM input) .. ok
170: Count -q 100 (SAM input) .. ok
171: Filter -q 100 (BAM input) .. ok
172: Count -q 100 (BAM input) .. ok
173: Filter -q 100 (CRAM input) .. ok
174: Count -q 100 (CRAM input) .. ok
175: Filter -x fa (SAM input) .. ok
176: Count -x fa (SAM input) .. ok
177: Filter -x fa (BAM input) .. ok
178: Count -x fa (BAM input) .. ok
179: Filter -x fa (CRAM input) .. ok
180: Count -x fa (CRAM input) .. ok
181: Filter -x fa -x ha (SAM input) .. ok
182: Count -x fa -x ha (SAM input) .. ok
183: Filter -x fa -x ha (BAM input) .. ok
184: Count -x fa -x ha (BAM input) .. ok
185: Filter -x fa -x ha (CRAM input) .. ok
186: Count -x fa -x ha (CRAM input) .. ok
187: Filter -x fa,ha (SAM input) .. ok
188: Count -x fa,ha (SAM input) .. ok
189: Filter -x fa,ha (BAM input) .. ok
190: Count -x fa,ha (BAM input) .. ok
191: Filter -x fa,ha (CRAM input) .. ok
192: Count -x fa,ha (CRAM input) .. ok
193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
205: Filter -x fa -r grp2 (SAM input) .. ok
206: Count -x fa -r grp2 (SAM input) .. ok
207: Filter -x fa -r grp2 (BAM input) .. ok
208: Count -x fa -r grp2 (BAM input) .. ok
209: Filter -x fa -r grp2 (CRAM input) .. ok
210: Count -x fa -r grp2 (CRAM input) .. ok
211: Filter -x RG -r grp2 (SAM input) .. ok
212: Count -x RG -r grp2 (SAM input) .. ok
213: Filter -x RG -r grp2 (BAM input) .. ok
214: Count -x RG -r grp2 (BAM input) .. ok
215: Filter -x RG -r grp2 (CRAM input) .. ok
216: Count -x RG -r grp2 (CRAM input) .. ok
217: Filter -m 10 (SAM input) .. ok
218: Count -m 10 (SAM input) .. ok
219: Filter -m 10 (BAM input) .. ok
220: Count -m 10 (BAM input) .. ok
221: Filter -m 10 (CRAM input) .. ok
222: Count -m 10 (CRAM input) .. ok
223: Filter -m 11 (SAM input) .. ok
224: Count -m 11 (SAM input) .. ok
225: Filter -m 11 (BAM input) .. ok
226: Count -m 11 (BAM input) .. ok
227: Filter -m 11 (CRAM input) .. ok
228: Count -m 11 (CRAM input) .. ok
229: Filter -m 15 (SAM input) .. ok
230: Count -m 15 (SAM input) .. ok
231: Filter -m 15 (BAM input) .. ok
232: Count -m 15 (BAM input) .. ok
233: Filter -m 15 (CRAM input) .. ok
234: Count -m 15 (CRAM input) .. ok
235: Filter -m 16 (SAM input) .. ok
236: Count -m 16 (SAM input) .. ok
237: Filter -m 16 (BAM input) .. ok
238: Count -m 16 (BAM input) .. ok
239: Filter -m 16 (CRAM input) .. ok
240: Count -m 16 (CRAM input) .. ok
241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok
242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok
243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok
244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok
245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok
246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok
247: Filter -e [BC] (SAM input) .. ok
248: Count -e [BC] (SAM input) .. ok
249: Filter -e [BC] (BAM input) .. ok
250: Count -e [BC] (BAM input) .. ok
251: Filter -e [BC] (CRAM input) .. ok
252: Count -e [BC] (CRAM input) .. ok
253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok
254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok
255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok
256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok
257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok
258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok
259: Filter -e mapq >= 50 (SAM input) .. ok
260: Count -e mapq >= 50 (SAM input) .. ok
261: Filter -e mapq >= 50 (BAM input) .. ok
262: Count -e mapq >= 50 (BAM input) .. ok
263: Filter -e mapq >= 50 (CRAM input) .. ok
264: Count -e mapq >= 50 (CRAM input) .. ok
265: Filter -e mapq >= 99 (SAM input) .. ok
266: Count -e mapq >= 99 (SAM input) .. ok
267: Filter -e mapq >= 99 (BAM input) .. ok
268: Count -e mapq >= 99 (BAM input) .. ok
269: Filter -e mapq >= 99 (CRAM input) .. ok
270: Count -e mapq >= 99 (CRAM input) .. ok
271: Filter -e mapq >= 100 (SAM input) .. ok
272: Count -e mapq >= 100 (SAM input) .. ok
273: Filter -e mapq >= 100 (BAM input) .. ok
274: Count -e mapq >= 100 (BAM input) .. ok
275: Filter -e mapq >= 100 (CRAM input) .. ok
276: Count -e mapq >= 100 (CRAM input) .. ok
277: 1bp reads file SAM -> BAM -> SAM .. ok
278: 1bp reads file SAM -> CRAM -> SAM .. ok
278: Region Z (BAM input) .. ok
279: Count Z (BAM input) .. ok
280: Region Z (CRAM input) .. ok
281: Count Z (CRAM input) .. ok
282: Region Z:30 (BAM input) .. ok
283: Count Z:30 (BAM input) .. ok
284: Region Z:30 (CRAM input) .. ok
285: Count Z:30 (CRAM input) .. ok
286: Region Z:20-40 (BAM input) .. ok
287: Count Z:20-40 (BAM input) .. ok
288: Region Z:20-40 (CRAM input) .. ok
289: Count Z:20-40 (CRAM input) .. ok
290: Region ref1 (BAM input) .. ok
291: Count ref1 (BAM input) .. ok
292: Region ref1 (CRAM input) .. ok
293: Count ref1 (CRAM input) .. ok
294: Region ref1:15 (BAM input) .. ok
295: Count ref1:15 (BAM input) .. ok
296: Region ref1:15 (CRAM input) .. ok
297: Count ref1:15 (CRAM input) .. ok
298: Region ref1:15-45 (BAM input) .. ok
299: Count ref1:15-45 (BAM input) .. ok
300: Region ref1:15-45 (CRAM input) .. ok
301: Count ref1:15-45 (CRAM input) .. ok
302: Region ref1:15-45 ref2 (BAM input) .. ok
303: Count ref1:15-45 ref2 (BAM input) .. ok
304: Region ref1:15-45 ref2 (CRAM input) .. ok
305: Count ref1:15-45 ref2 (CRAM input) .. ok
306: Region ref1:15-45 ref2:16 (BAM input) .. ok
307: Count ref1:15-45 ref2:16 (BAM input) .. ok
308: Region ref1:15-45 ref2:16 (CRAM input) .. ok
309: Count ref1:15-45 ref2:16 (CRAM input) .. ok
310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
318: Region -f 128 ref1 (BAM input) .. ok
319: Count -f 128 ref1 (BAM input) .. ok
320: Region -f 128 ref1 (CRAM input) .. ok
321: Count -f 128 ref1 (CRAM input) .. ok
322: Region -q 50 ref1:15-45 (BAM input) .. ok
323: Count -q 50 ref1:15-45 (BAM input) .. ok
324: Region -q 50 ref1:15-45 (CRAM input) .. ok
325: Count -q 50 ref1:15-45 (CRAM input) .. ok
326: Region -r grp2 ref1:15-45 (BAM input) .. ok
327: Count -r grp2 ref1:15-45 (BAM input) .. ok
328: Region -r grp2 ref1:15-45 (CRAM input) .. ok
329: Count -r grp2 ref1:15-45 (CRAM input) .. ok
330: Region * (BAM input) .. ok
331: Count * (BAM input) .. ok
332: Region * (CRAM input) .. ok
333: Count * (CRAM input) .. ok
334: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
335: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
336: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
337: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
338: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
339: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
340: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
341: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
342: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
343: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
344: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
345: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
346: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
347: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
348: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
349: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
350: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.03.bed (BAM input).. ok
351: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.03.bed (BAM input).. ok
352: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.03.bed (CRAM input).. ok
353: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.03.bed (CRAM input).. ok
354: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
355: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
356: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
357: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
358: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
359: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
360: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
361: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
362: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
363: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
364: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
365: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
366: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
367: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
368: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
369: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
370: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
371: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
372: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
373: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
374: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
375: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
376: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
377: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
378: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
379: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
380: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
381: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
382: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
383: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
384: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
385: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
386: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
387: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
388: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
389: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
390: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
391: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
392: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
393: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
394: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
395: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
396: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
397: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
398: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap (BAM input).. ok
399: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap (BAM input).. ok
400: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok
401: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok
402: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok
403: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok
404: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok
405: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok
406: Make BAM with no M5/UR tags .. ok
407: Add @SQ with -t (SAM -> SAM) .. ok
408: Add @SQ with -T (SAM -> SAM) .. ok
409: Add @SQ with -t (BAM -> SAM) .. ok
410: Add @SQ with -T (BAM -> SAM) .. ok
411: Add @SQ with -t (SAM -> BAM) .. ok
412: Add @SQ with -T (SAM -> BAM) .. ok
413: Add @SQ with -t (BAM -> BAM) .. ok
414: Add @SQ with -T (BAM -> BAM) .. ok
415: Add @SQ with -t (SAM -> CRAM) .. ok
416: Add @SQ with -T (SAM -> CRAM) .. ok
417: Add @SQ with -t (BAM -> CRAM) .. ok
418: Add @SQ with -T (BAM -> CRAM) .. ok
419: Make CRAM with no UR field .. ok
420: Decoding CRAM with no UR field via -T .. ok
421: CIGAR B-operator removal .. ok
422: Big SAM -> BAM .. ok
423: Big SAM -> BAM (2 threads) .. ok
424: Big SAM -> BAM (4 threads) .. ok
425: Big SAM -> CRAM .. ok
426: Big SAM -> CRAM (2 threads) .. ok
427: Big SAM -> CRAM (4 threads) .. ok
428: Subsample 0.2 (SAM input) ............ ok
429: Subsample 0.5 (SAM input) ............ ok
430: Subsample 0.8 (SAM input) ............ ok
431: Subsample 0.2 (BAM input) ............ ok
432: Subsample 0.5 (BAM input) ............ ok
433: Subsample 0.8 (BAM input) ............ ok
434: Subsample 0.2 (CRAM input) ............ ok
435: Subsample 0.5 (CRAM input) ............ ok
436: Subsample 0.8 (CRAM input) ............ ok
437: SAM add PG .. ok
438: Unset dup flag, remove dt and do tags .. ok
439: Unmap dup flagged reads. .. ok
440: Unmap dup flagged reads. .. ok
441: fetch pairs .. ok
442: fetch pairs .. ok
443: fetch pairs .. ok
test_head:
/<<PKGBUILDDIR>>/samtools head /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok
test_head:
/<<PKGBUILDDIR>>/samtools head -h 0 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok
test_head:
/<<PKGBUILDDIR>>/samtools head -h 1 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok
test_head:
/<<PKGBUILDDIR>>/samtools head -h 5 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok
test_head:
/<<PKGBUILDDIR>>/samtools head -h 29 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok
test_head:
/<<PKGBUILDDIR>>/samtools head -h 30 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok
test_head:
/<<PKGBUILDDIR>>/samtools head -n 0 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok
test_head:
/<<PKGBUILDDIR>>/samtools head -n 1 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok
test_head:
/<<PKGBUILDDIR>>/samtools head -n 5 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok
test_head:
/<<PKGBUILDDIR>>/samtools head -h 5 -n 5 < /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. 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_import:
/<<PKGBUILDDIR>>/samtools import -0 test/bam2fq/1.1.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -0 /<<PKGBUILDDIR>>/test/0.fq
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import -s test/bam2fq/1.1.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -0 /<<PKGBUILDDIR>>/test/0.fq
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import -s test/bam2fq/5.s.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -s /<<PKGBUILDDIR>>/test/s.fq
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -N -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -i --index-format 'i*i*' -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -N -T RG,BC,QT -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -N -T RG,BC,QT,MD,ia -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid'
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import test/import/2.interleaved.fq -T ""
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import test/import/3.interleaved.fq -i
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import test/import/4.aux.fq -T "*"
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import test/import/4.aux.fq -T ""
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import test/import/4.aux.fq -T XZ,XA,AA
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq
.. ok
test_import:
/<<PKGBUILDDIR>>/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ
.. ok
test_bam2fq:
Generate BAM file .. ok
Generate CRAM file .. ok
1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.002.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.003.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.010.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /<<PKGBUILDDIR>>/test/bc_split.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -t -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -t -T MD,ia -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -i --index-format 'i*i*' -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.703.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -1 /<<PKGBUILDDIR>>/test/o.fq -2 /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fasta -N -1 /<<PKGBUILDDIR>>/test/o.fa -2 /<<PKGBUILDDIR>>/test/o.fa /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -o /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -s /tmp/mx6BYkc173/bam2fq.discard.s.fq -0 /tmp/mx6BYkc173/bam2fq.discard.0.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -T ba,bb,bc,bd,be,bf,bg /<<PKGBUILDDIR>>/test/dat/bam2fq.013.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --index-format 'i8n1i8' --i1 /<<PKGBUILDDIR>>/test/i1.fq --i2 /<<PKGBUILDDIR>>/test/i2.fq -0 /<<PKGBUILDDIR>>/test/0.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.014.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -T '' /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -t -T '*' /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -T '*' -d MD:10 /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -T '*' -d NM:0 /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -N -T '*' -d ia /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
Generate BAM file (2 threads) .. ok
Generate CRAM file (2 threads) .. ok
1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.002.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.003.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.010.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /<<PKGBUILDDIR>>/test/bc_split.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -t -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -t -T MD,ia -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -i --index-format 'i*i*' -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.703.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -1 /<<PKGBUILDDIR>>/test/o.fq -2 /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fasta -@ 2 -N -1 /<<PKGBUILDDIR>>/test/o.fa -2 /<<PKGBUILDDIR>>/test/o.fa /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -o /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -s /tmp/mx6BYkc173/bam2fq.discard.s.fq -0 /tmp/mx6BYkc173/bam2fq.discard.0.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /<<PKGBUILDDIR>>/test/dat/bam2fq.013.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /<<PKGBUILDDIR>>/test/i1.fq --i2 /<<PKGBUILDDIR>>/test/i2.fq -0 /<<PKGBUILDDIR>>/test/0.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.014.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -T '' /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -t -T '*' /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -T '*' -d MD:10 /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -T '*' -d NM:0 /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -T '*' -d ia /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_depad:
Generate BAM file .. ok
depad (SAM input) .. ok
depad -s (SAM input) .. ok
depad -u (SAM input) .. ok
depad -1 (SAM input) .. ok
depad (BAM input) .. ok
depad -s (BAM input) .. ok
depad -u (BAM input) .. ok
depad -1 (BAM input) .. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/1_map_cigar_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/4_X_cigar_full_seq.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/5_insert_cigar_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa -i 0 /<<PKGBUILDDIR>>/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/7_supp_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/8_secondary_large.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -S RG -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -S RG -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -t /<<PKGBUILDDIR>>/test/stat/11.stats.targets /<<PKGBUILDDIR>>/test/stat/11_target.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -g 4 -t /<<PKGBUILDDIR>>/test/stat/11.stats.targets /<<PKGBUILDDIR>>/test/stat/11_target.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -g 4 /<<PKGBUILDDIR>>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -t /<<PKGBUILDDIR>>/test/stat/12_3reads.bed | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -p -t /<<PKGBUILDDIR>>/test/stat/12_3reads.bed | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -t /<<PKGBUILDDIR>>/test/stat/12_2reads.bed | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -p -t /<<PKGBUILDDIR>>/test/stat/12_2reads.bed | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_ok.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4
/<<PKGBUILDDIR>>/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4
/<<PKGBUILDDIR>>/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure
test_stats:
/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4
/<<PKGBUILDDIR>>/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure
test_stats:
/<<PKGBUILDDIR>>/samtools stats -I s1 /<<PKGBUILDDIR>>/test/stat/11_target.bam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -I grp2 /<<PKGBUILDDIR>>/test/stat/11_target.bam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -I grp3 /<<PKGBUILDDIR>>/test/stat/11_target.bam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -I Sample /<<PKGBUILDDIR>>/test/stat/11_target.bam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/mpileup/ce.fa /<<PKGBUILDDIR>>/test/stat/15.big_del.sam | tail -n+4
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam -b /tmp/3LWnAplEDb - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -r -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -cp -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a_regex.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b_regex.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -o - -s 1 -O sam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/mx6BYkc173/merge.tag.1.bam /tmp/mx6BYkc173/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/mx6BYkc173/merge.tag.3.bam /tmp/mx6BYkc173/merge.tag.4.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge --no-PG -O SAM - /<<PKGBUILDDIR>>/test/merge/test_no_pg_rg_co.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge --no-PG -O SAM -L /<<PKGBUILDDIR>>/test/merge/merge.bed - /tmp/mx6BYkc173/merge.bed.1.bam /tmp/mx6BYkc173/merge.bed.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge --no-PG -r -O SAM - /<<PKGBUILDDIR>>/test/merge/test_no_pg_rg_co.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam -b /tmp/JSvGqvmICZ - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -r -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -cp -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a_regex.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b_regex.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -o - -s 1 -O sam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/mx6BYkc173/merge.tag.1.bam /tmp/mx6BYkc173/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/mx6BYkc173/merge.tag.3.bam /tmp/mx6BYkc173/merge.tag.4.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 --no-PG -O SAM - /<<PKGBUILDDIR>>/test/merge/test_no_pg_rg_co.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 --no-PG -O SAM -L /<<PKGBUILDDIR>>/test/merge/merge.bed - /tmp/mx6BYkc173/merge.bed.1.bam /tmp/mx6BYkc173/merge.bed.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 --no-PG -r -O SAM - /<<PKGBUILDDIR>>/test/merge/test_no_pg_rg_co.sam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/mx6BYkc173/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/mx6BYkc173/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/mx6BYkc173/sorttmp
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -n -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -N -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -n -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -t AS -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -t FI -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort --template-coordinate -m 10M /<<PKGBUILDDIR>>/test/sort/template-coordinate.sort.sam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -M -K10 -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -M -K10 -I /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -MH -K10 -I /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/mx6BYkc173/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/mx6BYkc173/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/mx6BYkc173/sorttmp
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -n -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -N -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -n -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -t AS -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -t FI -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 --template-coordinate -m 10M /<<PKGBUILDDIR>>/test/sort/template-coordinate.sort.sam -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -@ 2 -M -K10 -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -@ 2 -M -K10 -I /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa -O SAM -o -
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -@ 2 -MH -K10 -I /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa -O SAM -o -
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam -O /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -o /<<PKGBUILDDIR>>/test/collate/collate1.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -o /<<PKGBUILDDIR>>/test/collate/collate2.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate2.tmp
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate3.tmp
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam -f /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/1_fast_collate.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam -f -r 4 /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/2_fast_collate_with_tmp.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam -O /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 -o /<<PKGBUILDDIR>>/test/collate/collate1.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 -o /<<PKGBUILDDIR>>/test/collate/collate2.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate2.tmp
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate3.tmp
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam -f /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/1_fast_collate.sam
.. ok
test_collate:
/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam -f -r 4 /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/2_fast_collate_with_tmp.sam
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/1_coord_sort.sam -
ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
.. expected failure
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -z off -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 -z off -O sam /<<PKGBUILDDIR>>/test/fixmate/7_two_read_mapped.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -z off -O sam /<<PKGBUILDDIR>>/test/fixmate/8_isize_overflow_64bit.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/sanitize.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 -z off -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 -z off -O sam /<<PKGBUILDDIR>>/test/fixmate/7_two_read_mapped.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -z off -O sam /<<PKGBUILDDIR>>/test/fixmate/8_isize_overflow_64bit.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/sanitize.sam -
.. ok
/<<PKGBUILDDIR>>/samtools calmd -uAr /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa
.. ok
/<<PKGBUILDDIR>>/samtools calmd -@ 2 -uAr /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa
.. ok
test_idxstat:
/<<PKGBUILDDIR>>/samtools idxstats /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_idxstat:
/<<PKGBUILDDIR>>/samtools idxstats /<<PKGBUILDDIR>>/test/dat/test_input_1_a.cram
.. ok
test_idxstat:
/<<PKGBUILDDIR>>/samtools idxstats /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/1.quickcheck.badeof.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/2.quickcheck.badheader.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/3.quickcheck.ok.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/4.quickcheck.ok.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/5.quickcheck.scramble30.truncated.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/6.quickcheck.cram21.ok.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/7.quickcheck.cram30.ok.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/8.quickcheck.cram21.truncated.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/9.quickcheck.cram30.truncated.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/10.quickcheck.notargets.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck -v /<<PKGBUILDDIR>>/test/quickcheck/1.quickcheck.badeof.bam /<<PKGBUILDDIR>>/test/quickcheck/2.quickcheck.badheader.bam /<<PKGBUILDDIR>>/test/quickcheck/3.quickcheck.ok.bam /<<PKGBUILDDIR>>/test/quickcheck/4.quickcheck.ok.bam /<<PKGBUILDDIR>>/test/quickcheck/5.quickcheck.scramble30.truncated.cram /<<PKGBUILDDIR>>/test/quickcheck/6.quickcheck.cram21.ok.cram /<<PKGBUILDDIR>>/test/quickcheck/7.quickcheck.cram30.ok.cram /<<PKGBUILDDIR>>/test/quickcheck/8.quickcheck.cram21.truncated.cram /<<PKGBUILDDIR>>/test/quickcheck/9.quickcheck.cram30.truncated.cram /<<PKGBUILDDIR>>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck -uv /<<PKGBUILDDIR>>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.bam | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader --in-place /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram && /<<PKGBUILDDIR>>/samtools view -h --no-PG /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader --in-place /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram && /<<PKGBUILDDIR>>/samtools view -h --no-PG /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<<PKGBUILDDIR>>/test/dat/view.001.tmp.bam | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m overwrite_all /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m orphan_only /<<PKGBUILDDIR>>/test/addrprg/2_fixup_orphan.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -R '1#9' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m overwrite_all /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m orphan_only /<<PKGBUILDDIR>>/test/addrprg/2_fixup_orphan.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -R '1#9' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/1_name_sort.sam -
ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/2_bad_order.sam -
ERR: samtools markdup: error, not in coordinate sorted order.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/3_missing_mc.sam -
ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.
samtools markdup: error, unable to assign pair hash key.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/4_missing_ms.sam -
ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.
samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/5_markdup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -O sam -r --no-PG /<<PKGBUILDDIR>>/test/markdup/6_remove_dups.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/7_mark_supp_dup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/8_optical_dup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/9_optical_dup_qcfail.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /<<PKGBUILDDIR>>/test/markdup/10_optical_chain.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /<<PKGBUILDDIR>>/test/markdup/10_optical_chain.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /<<PKGBUILDDIR>>/test/markdup/11_optical_dup_regex.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /<<PKGBUILDDIR>>/test/markdup/11_optical_dup_regex.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /<<PKGBUILDDIR>>/test/markdup/12_optical_chain_regex.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/13_optical_barcode_tag.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/14_optical_barcode_name.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/17_read_group.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /<<PKGBUILDDIR>>/test/markdup/18_primary_duplicate_count.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/1_name_sort.sam -
ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/2_bad_order.sam -
ERR: samtools markdup: error, not in coordinate sorted order.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/3_missing_mc.sam -
ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.
samtools markdup: error, unable to assign pair hash key.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/4_missing_ms.sam -
ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.
samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.
.. expected failure
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/5_markdup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam -r --no-PG /<<PKGBUILDDIR>>/test/markdup/6_remove_dups.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/7_mark_supp_dup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/8_optical_dup.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/9_optical_dup_qcfail.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /<<PKGBUILDDIR>>/test/markdup/10_optical_chain.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /<<PKGBUILDDIR>>/test/markdup/10_optical_chain.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /<<PKGBUILDDIR>>/test/markdup/11_optical_dup_regex.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /<<PKGBUILDDIR>>/test/markdup/11_optical_dup_regex.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /<<PKGBUILDDIR>>/test/markdup/12_optical_chain_regex.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/13_optical_barcode_tag.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/14_optical_barcode_name.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/17_read_group.sam -
.. ok
test_markdup:
/<<PKGBUILDDIR>>/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /<<PKGBUILDDIR>>/test/markdup/18_primary_duplicate_count.sam -
.. ok
test_bedcov:
/<<PKGBUILDDIR>>/samtools bedcov /<<PKGBUILDDIR>>/test/bedcov/bedcov.bed /<<PKGBUILDDIR>>/test/bedcov/bedcov.bam
.. ok
test_bedcov:
/<<PKGBUILDDIR>>/samtools bedcov -j /<<PKGBUILDDIR>>/test/bedcov/bedcov.bed /<<PKGBUILDDIR>>/test/bedcov/bedcov.bam
.. ok
test_bedcov:
/<<PKGBUILDDIR>>/samtools bedcov -g512 -G2048 /<<PKGBUILDDIR>>/test/bedcov/bedcov_gG.bed /<<PKGBUILDDIR>>/test/bedcov/bedcov.bam
.. ok
test_bedcov:
/<<PKGBUILDDIR>>/samtools bedcov -c /<<PKGBUILDDIR>>/test/bedcov/bedcov_gG.bed /<<PKGBUILDDIR>>/test/bedcov/bedcov.bam
.. ok
test_split:
/<<PKGBUILDDIR>>/samtools split --output-fmt sam -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok
test_split:
/<<PKGBUILDDIR>>/samtools split --output-fmt sam -d RG -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok
test_split:
/<<PKGBUILDDIR>>/samtools split --output-fmt sam -d an -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok
test_split:
/<<PKGBUILDDIR>>/samtools split --output-fmt sam -d an -M 3 -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok
test_split:
/<<PKGBUILDDIR>>/samtools split -@ 2 --output-fmt sam -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok
test_split:
/<<PKGBUILDDIR>>/samtools split -@ 2 --output-fmt sam -d RG -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok
test_split:
/<<PKGBUILDDIR>>/samtools split -@ 2 --output-fmt sam -d an -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok
test_split:
/<<PKGBUILDDIR>>/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools view -h --no-PG /tmp/mx6BYkc173/longref.sam.gz
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools view -h --no-PG /tmp/mx6BYkc173/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools view -h --no-PG -L /<<PKGBUILDDIR>>/test/large_pos/test.bed /tmp/mx6BYkc173/longref.sam.gz
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools sort -O sam --no-PG -m 10M /<<PKGBUILDDIR>>/test/large_pos/longref_name.sam
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools merge -O sam --no-PG - /<<PKGBUILDDIR>>/test/large_pos/longref.sam /<<PKGBUILDDIR>>/test/large_pos/longref2.sam
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools depth /<<PKGBUILDDIR>>/test/large_pos/longref.sam
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools depth -b /<<PKGBUILDDIR>>/test/large_pos/test.bed /<<PKGBUILDDIR>>/test/large_pos/longref.sam
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/mx6BYkc173/longref.sam.gz
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam |
/<<PKGBUILDDIR>>/samtools fixmate -O sam --no-PG - - |
/<<PKGBUILDDIR>>/samtools sort -O sam --no-PG -m 10M
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/2_both_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test2.bed /<<PKGBUILDDIR>>/test/ampliconclip/4_total_hc_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/2_both_test_data.sam
.. ok
test_ampliconclip:
/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test2.bed /<<PKGBUILDDIR>>/test/ampliconclip/4_total_hc_data.sam
.. ok
test_ampliconstats:
/<<PKGBUILDDIR>>/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_hard_clipped.expected.sam /<<PKGBUILDDIR>>/test/ampliconclip/1_soft_clipped.expected.sam /<<PKGBUILDDIR>>/test/ampliconclip/1_soft_clipped_strand.expected.sam /<<PKGBUILDDIR>>/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line'
.. ok
test_ampliconstats:
/<<PKGBUILDDIR>>/samtools ampliconstats -@ 2 -c 0 /<<PKGBUILDDIR>>/test/ampliconclip/multi_ref.bed /<<PKGBUILDDIR>>/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
.. ok
test_ampliconstats:
/<<PKGBUILDDIR>>/samtools ampliconstats -@ 2 -c 0 /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
.. ok
test_reset:
cat /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam | /<<PKGBUILDDIR>>/samtools reset | /<<PKGBUILDDIR>>/samtools view
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset < /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam | /<<PKGBUILDDIR>>/samtools view
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam | /<<PKGBUILDDIR>>/samtools view
.. ok
test_reset:
cat /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam | /<<PKGBUILDDIR>>/samtools reset -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.cram
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa_index /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam; grep /<<PKGBUILDDIR>>/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g'
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset --reject-PG sam_to_fixed_bam /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam; grep /<<PKGBUILDDIR>>/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g'
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa_index --no-PG /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam; grep /<<PKGBUILDDIR>>/test/reset/output.tmp.sam -e"@PG"
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG -o /<<PKGBUILDDIR>>/test/reset/output
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /<<PKGBUILDDIR>>/test/reset/output
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /<<PKGBUILDDIR>>/test/reset/output
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /<<PKGBUILDDIR>>/test/reset/output
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /<<PKGBUILDDIR>>/test/reset/output
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /<<PKGBUILDDIR>>/test/reset/output
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /<<PKGBUILDDIR>>/test/reset/output
.. ok
test_reset:
/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/reset/seq.sam -o /<<PKGBUILDDIR>>/test/reset/output
.. ok
Number of tests:
total .. 933
passed .. 889
failed .. 0
expected failure .. 44
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg
=== Testing mpileup.reg regressions ===
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam
Expected passes: 118
Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
cd test/mpileup && AWK="mawk" ../regression.sh depth.reg
=== Testing depth.reg regressions ===
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools depth -a -b xx.bed3 xx#depth3.bam
Expected passes: 53
Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
cd test/consensus && AWK="mawk" ../regression.sh consensus.reg
=== Testing consensus.reg regressions ===
Expected passes: 65
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
=> PASS
cd test/cram_size && AWK="mawk" ../regression.sh cram_size.reg
=== Testing cram_size.reg regressions ===
Expected passes: 3
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
=> PASS
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -fr -- /tmp/dh-xdg-rundir-im7GBR2h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
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 -m0755 -d /<<PKGBUILDDIR>>/debian/tmp
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
make[2]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp/usr/bin /<<PKGBUILDDIR>>/debian/tmp/usr/bin /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
install -p samtools /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p -m 644 doc/samtools*.1 misc/wgsim.1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd test/dat && rm -f test_input_*.bam.bai view.*.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*
cd test/reference && rm -f mpileup.*.fai
rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o
rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/samtools.debhelper.log
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
install -m0755 -d debian/samtools//usr
cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
install -m0755 -d debian/samtools//usr/share/man
cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
install -m0755 -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//
install -m0755 -d debian/samtools/usr/share/man/man1
cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
# Fix Perl interpreter PATH
for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \
sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \
done
# Disable the executable bit on a dataset.
if [ -d debian/samtools-test ] \
; then chmod 0644 debian/samtools-test/usr/share/samtools/test/ampliconclip/ac_test.bed \
; fi
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
install -m0755 -d debian/samtools/usr/share/doc/samtools
install -m0755 -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a ./AUTHORS debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a ./README debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a ./debian/README.test debian/samtools/usr/share/doc/samtools
chmod -R u\+rw,go=rX debian/samtools/usr/share/doc
install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
rm -f debian/samtools.debhelper.log
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs NEWS.md
install -m0755 -d debian/samtools/usr/share/doc/samtools
install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian
install -p -m0644 NEWS.md debian/samtools/usr/share/doc/samtools/changelog
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installexamples -a
install -m0755 -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
rm -f debian/samtools.debhelper.log
debian/rules execute_before_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# Fix whatis entries for subcommands; "samtools subcommand \- desc."
# will confuse the lexer, but "samtools-subcommand \- desc." will work.
sed -i '/^\.SH NAME/{n;s/^\([^ ]\+\) \([^ ]\+\) \\- /\1-\2 \\- /}' \
debian/*/usr/share/man/man*/*.*
# .EX expects a indentation width.
sed -i 's/^.EX$/.EX 8/' debian/*/usr/share/man/man*/*.*
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installman -a
rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1
ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1
man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1
man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1
man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1
man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1
mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1
mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1
mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1
mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1
mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1
mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1
mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1
mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1
mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1
mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1
chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1
mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1
mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1
mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1
mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1
mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1
mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1
mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1
mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1
mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1
mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1
mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1
chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1
mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1
mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1
mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1
mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1
mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1
mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1
mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1
mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1
mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1
mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1
mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1
chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1
mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1
mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1
mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1
mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1
mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1
mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1
mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1
mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1
mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1
mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1
mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1
chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1
dh_lintian -a
install -m0755 -d debian/samtools/usr/share/lintian/overrides
install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a
rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1
ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1
dh_strip_nondeterminism -a
Using 1708190561 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/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
gzip -9nf usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/<<PKGBUILDDIR>>'
rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz
ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz
dh_fixperms -a
find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing -a
dh_dwz -a
install -m0755 -d debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -mdebian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim
dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 722485 new size 744864
objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
dh_strip -a
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3f
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3f/f517cec0093340f0068eed2e261280e2efea88.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3f/f517cec0093340f0068eed2e261280e2efea88.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/3f/f517cec0093340f0068eed2e261280e2efea88.debug debian/samtools/usr/bin/samtools
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/af
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/af/519bd3e0ea26cb792c7f89541d4abf6f508dd1.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/af/519bd3e0ea26cb792c7f89541d4abf6f508dd1.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/af/519bd3e0ea26cb792c7f89541d4abf6f508dd1.debug debian/samtools/usr/bin/maq2sam-long
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bf
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bf/881a0c5ee1d64159f2db493a3970fea02b4347.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bf/881a0c5ee1d64159f2db493a3970fea02b4347.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/bf/881a0c5ee1d64159f2db493a3970fea02b4347.debug debian/samtools/usr/bin/ace2sam
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3a
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3a/8c4bc555185522278a920a37b0df9bd15d4e27.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3a/8c4bc555185522278a920a37b0df9bd15d4e27.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/3a/8c4bc555185522278a920a37b0df9bd15d4e27.debug debian/samtools/usr/bin/maq2sam-short
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/ea185465e90ee18f4fa055b81b6814aebdff90.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/ea185465e90ee18f4fa055b81b6814aebdff90.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/30/ea185465e90ee18f4fa055b81b6814aebdff90.debug debian/samtools/usr/bin/md5fa
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/05
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/05/719ebb42e7a886b1da40965cf37d1411700584.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/05/719ebb42e7a886b1da40965cf37d1411700584.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/05/719ebb42e7a886b1da40965cf37d1411700584.debug debian/samtools/usr/bin/md5sum-lite
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c0
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c0/af496be6a0c7011138a80fe4e58a609e756585.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c0/af496be6a0c7011138a80fe4e58a609e756585.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/c0/af496be6a0c7011138a80fe4e58a609e756585.debug debian/samtools/usr/bin/wgsim
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/samtools/usr/lib/debug/.dwz
rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym
install -m0755 -d debian/.debhelper/samtools
dh_makeshlibs -a
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
install -m0755 -d debian/samtools/DEBIAN
dh_gencontrol -a
install -m0755 -d debian/samtools/DEBIAN
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=05719ebb42e7a886b1da40965cf37d1411700584 30ea185465e90ee18f4fa055b81b6814aebdff90 3a8c4bc555185522278a920a37b0df9bd15d4e27 3ff517cec0093340f0068eed2e261280e2efea88 af519bd3e0ea26cb792c7f89541d4abf6f508dd1 bf881a0c5ee1d64159f2db493a3970fea02b4347 c0af496be6a0c7011138a80fe4e58a609e756585" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined
chmod 0644 -- debian/samtools/DEBIAN/control
dh_md5sums -a
install -m0755 -d debian/samtools/DEBIAN
cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/samtools/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --root-owner-group --build debian/samtools ..
dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root ..
dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.19.2-1_armhf.deb'.
dpkg-deb: building package 'samtools' in '../samtools_1.19.2-1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../samtools_1.19.2-1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../samtools_1.19.2-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from samtools-1.19.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2024-02-20T06:08:16Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
samtools_1.19.2-1_armhf.changes:
--------------------------------
Format: 1.8
Date: Sat, 17 Feb 2024 18:22:41 +0100
Source: samtools
Binary: samtools samtools-dbgsym
Architecture: armhf
Version: 1.19.2-1
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
samtools - processing sequence alignments in SAM, BAM and CRAM formats
Changes:
samtools (1.19.2-1) unstable; urgency=medium
.
* [3f34445] New upstream version 1.19.2
* [e0d4f37] d/control: replace pkg-config by pkgconf.
Checksums-Sha1:
4f44d0979559f0dc19a257ad6eda7f94544a44a0 930264 samtools-dbgsym_1.19.2-1_armhf.deb
a183abc2ded0fd265a1dd61e17850562dc5b8cc2 6209 samtools_1.19.2-1_armhf.buildinfo
3bdd0fb666a56a842a45738e2af959a9658426b0 594324 samtools_1.19.2-1_armhf.deb
Checksums-Sha256:
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3c8175cf99a4200837e9b9ea01a83b1dac999c70bdd5a726149b8af1e43da505 6209 samtools_1.19.2-1_armhf.buildinfo
2a23d0b6ee588ca84267bf0ca5925220e1807eadab7a9b6be6e6f3b1f5063647 594324 samtools_1.19.2-1_armhf.deb
Files:
9c6092b1dccacc445ebee0076b853913 930264 debug optional samtools-dbgsym_1.19.2-1_armhf.deb
459731d22a5fba0fa496768449a9509c 6209 science optional samtools_1.19.2-1_armhf.buildinfo
4544d11d27cf25e3e00229c8062c257a 594324 science optional samtools_1.19.2-1_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: samtools
Binary: samtools samtools-dbgsym
Architecture: armhf
Version: 1.19.2-1
Checksums-Md5:
9c6092b1dccacc445ebee0076b853913 930264 samtools-dbgsym_1.19.2-1_armhf.deb
4544d11d27cf25e3e00229c8062c257a 594324 samtools_1.19.2-1_armhf.deb
Checksums-Sha1:
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3bdd0fb666a56a842a45738e2af959a9658426b0 594324 samtools_1.19.2-1_armhf.deb
Checksums-Sha256:
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2a23d0b6ee588ca84267bf0ca5925220e1807eadab7a9b6be6e6f3b1f5063647 594324 samtools_1.19.2-1_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Tue, 20 Feb 2024 06:08:15 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
autoconf (= 2.71-3),
autoconf-archive (= 20220903-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-14),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.3),
bash (= 5.2.21-2),
bash-completion (= 1:2.11-8),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.3-6),
bsdutils (= 1:2.39.3-6),
build-essential (= 12.10),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.4-3),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-13+rpi1),
cpp-13 (= 13.2.0-9+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.83),
debhelper (= 13.13),
debianutils (= 5.16),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
dpkg (= 1.22.2+rpi1),
dpkg-dev (= 1.22.2+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-9+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-13+rpi1),
gcc-12-base (= 12.3.0-13+rpi1),
gcc-13 (= 13.2.0-9+rpi1),
gcc-13-base (= 13.2.0-9+rpi1),
gettext (= 0.21-14),
gettext-base (= 0.21-14),
grep (= 3.11-4),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
hostname (= 3.23+nmu2),
init-system-helpers (= 1.66),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-6),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 13.2.0-9+rpi1),
libatomic1 (= 13.2.0-9+rpi1),
libattr1 (= 1:2.5.1-5),
libaudit-common (= 1:3.1.2-1),
libaudit1 (= 1:3.1.2-1),
libbinutils (= 2.41-6+rpi1),
libblkid1 (= 2.39.3-6),
libbrotli1 (= 1.1.0-2),
libbz2-1.0 (= 1.0.8-5+b2),
libbz2-dev (= 1.0.8-5+b2),
libc-bin (= 2.37-13+rpi1),
libc-dev-bin (= 2.37-13+rpi1),
libc6 (= 2.37-13+rpi1),
libc6-dev (= 2.37-13+rpi1),
libcap-ng0 (= 0.8.4-1),
libcap2 (= 1:2.66-4),
libcc1-0 (= 13.2.0-9+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-4),
libcrypt1 (= 1:4.4.36-4),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libcurl3-gnutls (= 8.5.0-2+rpi1),
libcurl4-gnutls-dev (= 8.5.0-2+rpi1),
libdb5.3 (= 5.3.28+dfsg2-4),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.13),
libdeflate-dev (= 1.19-1),
libdeflate0 (= 1.19-1),
libdpkg-perl (= 1.22.2+rpi1),
libelf1 (= 0.188-2.1+rpi1),
libffi8 (= 3.4.4-2),
libfile-find-rule-perl (= 0.34-3),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libgcc-12-dev (= 12.3.0-13+rpi1),
libgcc-13-dev (= 13.2.0-9+rpi1),
libgcc-s1 (= 13.2.0-9+rpi1),
libgcrypt20 (= 1.10.3-2),
libgdbm-compat4 (= 1.23-5),
libgdbm6 (= 1.23-5),
libgmp10 (= 2:6.3.0+dfsg-2),
libgnutls30 (= 3.8.3-1),
libgomp1 (= 13.2.0-9+rpi1),
libgpg-error0 (= 1.47-3),
libgssapi-krb5-2 (= 1.20.1-5),
libhogweed6 (= 3.9.1-2),
libhts-dev (= 1.18+ds-1),
libhts3 (= 1.18+ds-1),
libhtscodecs2 (= 1.6.0-1),
libicu72 (= 72.1-4),
libidn2-0 (= 2.3.4-1),
libio-pty-perl (= 1:1.20-1),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libk5crypto3 (= 1.20.1-5),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-5),
libkrb5support0 (= 1.20.1-5),
libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1+b1),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma-dev (= 5.4.5-0.3),
liblzma5 (= 5.4.5-0.3),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmd0 (= 1.1.0-2),
libmount1 (= 2.39.3-6),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libncurses-dev (= 6.4+20240113-1),
libncurses6 (= 6.4+20240113-1),
libncursesw6 (= 6.4+20240113-1),
libnettle8 (= 3.9.1-2),
libnghttp2-14 (= 1.59.0-1),
libnsl-dev (= 1.3.0-3),
libnsl2 (= 1.3.0-3),
libnumber-compare-perl (= 0.03-3),
libp11-kit0 (= 0.25.3-4),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpcre2-8-0 (= 10.42-4),
libperl5.38 (= 5.38.2-3),
libpipeline1 (= 1.5.7-1),
libpkgconf3 (= 1.8.1-1),
libpsl5 (= 0.21.2-1+b1),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg1-4),
libsasl2-modules-db (= 2.1.28+dfsg1-4),
libseccomp2 (= 2.5.4-2+rpi1),
libselinux1 (= 3.5-1),
libsframe1 (= 2.41-6+rpi1),
libsmartcols1 (= 2.39.3-6),
libssh2-1 (= 1.11.0-4),
libssl3 (= 3.1.4-2),
libstdc++-13-dev (= 13.2.0-9+rpi1),
libstdc++6 (= 13.2.0-9+rpi1),
libsub-override-perl (= 0.10-1),
libsystemd0 (= 254.5-1+rpi1),
libtasn1-6 (= 4.19.0-3),
libtext-glob-perl (= 0.11-3),
libtinfo6 (= 6.4+20240113-1),
libtirpc-common (= 1.3.4+ds-1),
libtirpc-dev (= 1.3.4+ds-1),
libtirpc3 (= 1.3.4+ds-1),
libtool (= 2.4.7-7),
libubsan1 (= 13.2.0-9+rpi1),
libuchardet0 (= 0.0.8-1),
libudev1 (= 254.5-1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.3-6),
libxml2 (= 2.9.14+dfsg-1.3),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1+b1),
login (= 1:4.13+dfsg1-3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.0-3),
mawk (= 1.3.4.20231126-1),
ncurses-base (= 6.4+20240113-1),
ncurses-bin (= 6.4+20240113-1),
patch (= 2.7.6-7),
perl (= 5.38.2-3),
perl-base (= 5.38.2-3),
perl-modules-5.38 (= 5.38.2-3),
pkgconf (= 1.8.1-1),
pkgconf-bin (= 1.8.1-1),
po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-2),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-5),
tabix (= 1.18+ds-1),
tar (= 1.35+dfsg-3),
usrmerge (= 39),
util-linux (= 2.39.3-6),
xz-utils (= 5.4.5-0.3),
zlib1g (= 1:1.3.dfsg-3),
zlib1g-dev (= 1:1.3.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1708190561"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
samtools-dbgsym_1.19.2-1_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 930264 bytes: control archive=904 bytes.
623 bytes, 12 lines control
830 bytes, 8 lines md5sums
Package: samtools-dbgsym
Source: samtools
Version: 1.19.2-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1006
Depends: samtools (= 1.19.2-1)
Section: debug
Priority: optional
Description: debug symbols for samtools
Build-Ids: 05719ebb42e7a886b1da40965cf37d1411700584 30ea185465e90ee18f4fa055b81b6814aebdff90 3a8c4bc555185522278a920a37b0df9bd15d4e27 3ff517cec0093340f0068eed2e261280e2efea88 af519bd3e0ea26cb792c7f89541d4abf6f508dd1 bf881a0c5ee1d64159f2db493a3970fea02b4347 c0af496be6a0c7011138a80fe4e58a609e756585
drwxr-xr-x root/root 0 2024-02-17 17:22 ./
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/debug/.build-id/05/
-rw-r--r-- root/root 7256 2024-02-17 17:22 ./usr/lib/debug/.build-id/05/719ebb42e7a886b1da40965cf37d1411700584.debug
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/debug/.build-id/30/
-rw-r--r-- root/root 10524 2024-02-17 17:22 ./usr/lib/debug/.build-id/30/ea185465e90ee18f4fa055b81b6814aebdff90.debug
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/debug/.build-id/3a/
-rw-r--r-- root/root 10780 2024-02-17 17:22 ./usr/lib/debug/.build-id/3a/8c4bc555185522278a920a37b0df9bd15d4e27.debug
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/debug/.build-id/3f/
-rw-r--r-- root/root 916484 2024-02-17 17:22 ./usr/lib/debug/.build-id/3f/f517cec0093340f0068eed2e261280e2efea88.debug
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/debug/.build-id/af/
-rw-r--r-- root/root 10784 2024-02-17 17:22 ./usr/lib/debug/.build-id/af/519bd3e0ea26cb792c7f89541d4abf6f508dd1.debug
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root 24688 2024-02-17 17:22 ./usr/lib/debug/.build-id/bf/881a0c5ee1d64159f2db493a3970fea02b4347.debug
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/debug/.build-id/c0/
-rw-r--r-- root/root 22200 2024-02-17 17:22 ./usr/lib/debug/.build-id/c0/af496be6a0c7011138a80fe4e58a609e756585.debug
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 3604 2024-02-17 17:22 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-02-17 17:22 ./usr/share/doc/samtools-dbgsym -> samtools
samtools_1.19.2-1_armhf.deb
---------------------------
new Debian package, version 2.0.
size 594324 bytes: control archive=2940 bytes.
836 bytes, 17 lines control
5675 bytes, 83 lines md5sums
Package: samtools
Version: 1.19.2-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1257
Depends: libc6 (>= 2.34), libhts3 (>= 1.17), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.2.3.3)
Suggests: cwltool
Section: science
Priority: optional
Homepage: https://www.htslib.org/
Description: processing sequence alignments in SAM, BAM and CRAM formats
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) and CRAM formats, does sorting, merging and indexing,
and allows one to retrieve reads in any regions swiftly. It is designed to work
on a stream, and is able to open a BAM or CRAM (not SAM) file on a remote FTP
or HTTP server.
drwxr-xr-x root/root 0 2024-02-17 17:22 ./
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/bin/
-rwxr-xr-x root/root 18012 2024-02-17 17:22 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5443 2024-02-17 17:22 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3360 2024-02-17 17:22 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 17996 2024-02-17 17:22 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 3300 2024-02-17 17:22 ./usr/bin/fasta-sanitize.pl
-rwxr-xr-x root/root 6121 2024-02-17 17:22 ./usr/bin/interpolate_sam.pl
-rwxr-xr-x root/root 9820 2024-02-17 17:22 ./usr/bin/maq2sam-long
-rwxr-xr-x root/root 9820 2024-02-17 17:22 ./usr/bin/maq2sam-short
-rwxr-xr-x root/root 9820 2024-02-17 17:22 ./usr/bin/md5fa
-rwxr-xr-x root/root 5724 2024-02-17 17:22 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 7969 2024-02-17 17:22 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 44331 2024-02-17 17:22 ./usr/bin/plot-ampliconstats
-rwxr-xr-x root/root 55292 2024-02-17 17:22 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3204 2024-02-17 17:22 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8957 2024-02-17 17:22 ./usr/bin/sam2vcf.pl
-rwxr-xr-x root/root 647800 2024-02-17 17:22 ./usr/bin/samtools
-rwxr-xr-x root/root 16474 2024-02-17 17:22 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11333 2024-02-17 17:22 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3905 2024-02-17 17:22 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 18052 2024-02-17 17:22 ./usr/bin/wgsim
-rwxr-xr-x root/root 12542 2024-02-17 17:22 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3579 2024-02-17 17:22 ./usr/bin/zoom2sam.pl
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/commonwl/
-rwxr-xr-x root/root 1906 2023-12-15 15:06 ./usr/share/commonwl/samtools-faidx.cwl
-rwxr-xr-x root/root 1979 2023-12-15 15:06 ./usr/share/commonwl/samtools-index.cwl
-rwxr-xr-x root/root 1627 2023-12-15 15:06 ./usr/share/commonwl/samtools-rmdup.cwl
-rwxr-xr-x root/root 2834 2023-12-15 15:06 ./usr/share/commonwl/samtools-sort.cwl
-rwxr-xr-x root/root 6224 2023-12-15 15:06 ./usr/share/commonwl/samtools-view.cwl
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2024-01-24 09:34 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 497 2023-12-15 15:06 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 2482 2024-01-24 09:34 ./usr/share/doc/samtools/README.gz
-rw-r--r-- root/root 313 2023-12-15 15:06 ./usr/share/doc/samtools/README.test
-rw-r--r-- root/root 1973 2024-02-17 17:22 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 35525 2024-01-24 09:34 ./usr/share/doc/samtools/changelog.gz
-rw-r--r-- root/root 2250 2024-02-17 17:08 ./usr/share/doc/samtools/copyright
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 1315 2024-01-24 09:34 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 3225 2024-01-24 09:34 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2024-02-17 17:22 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 98 2024-01-24 09:34 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2024-01-24 09:34 ./usr/share/doc/samtools/examples/toy.sam
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/lintian/
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 168 2023-12-15 15:06 ./usr/share/lintian/overrides/samtools
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/man/
drwxr-xr-x root/root 0 2024-02-17 17:22 ./usr/share/man/man1/
-rw-r--r-- root/root 462 2024-02-17 17:22 ./usr/share/man/man1/ace2sam.1.gz
-rw-r--r-- root/root 1641 2024-02-17 17:22 ./usr/share/man/man1/samtools-addreplacerg.1.gz
-rw-r--r-- root/root 2358 2024-02-17 17:22 ./usr/share/man/man1/samtools-ampliconclip.1.gz
-rw-r--r-- root/root 5840 2024-02-17 17:22 ./usr/share/man/man1/samtools-ampliconstats.1.gz
-rw-r--r-- root/root 2021 2024-02-17 17:22 ./usr/share/man/man1/samtools-bedcov.1.gz
-rw-r--r-- root/root 2304 2024-02-17 17:22 ./usr/share/man/man1/samtools-calmd.1.gz
-rw-r--r-- root/root 1545 2024-02-17 17:22 ./usr/share/man/man1/samtools-cat.1.gz
-rw-r--r-- root/root 2478 2024-02-17 17:22 ./usr/share/man/man1/samtools-collate.1.gz
-rw-r--r-- root/root 6076 2024-02-17 17:22 ./usr/share/man/man1/samtools-consensus.1.gz
-rw-r--r-- root/root 2689 2024-02-17 17:22 ./usr/share/man/man1/samtools-coverage.1.gz
-rw-r--r-- root/root 3180 2024-02-17 17:22 ./usr/share/man/man1/samtools-cram-size.1.gz
-rw-r--r-- root/root 1756 2024-02-17 17:22 ./usr/share/man/man1/samtools-depad.1.gz
-rw-r--r-- root/root 3190 2024-02-17 17:22 ./usr/share/man/man1/samtools-depth.1.gz
-rw-r--r-- root/root 1686 2024-02-17 17:22 ./usr/share/man/man1/samtools-dict.1.gz
-rw-r--r-- root/root 2121 2024-02-17 17:22 ./usr/share/man/man1/samtools-faidx.1.gz
-rw-r--r-- root/root 4255 2024-02-17 17:22 ./usr/share/man/man1/samtools-fasta.1.gz
lrwxrwxrwx root/root 0 2024-02-17 17:22 ./usr/share/man/man1/samtools-fastq.1.gz -> samtools-fasta.1.gz
-rw-r--r-- root/root 1654 2024-02-17 17:22 ./usr/share/man/man1/samtools-fixmate.1.gz
-rw-r--r-- root/root 1500 2024-02-17 17:22 ./usr/share/man/man1/samtools-flags.1.gz
-rw-r--r-- root/root 2603 2024-02-17 17:22 ./usr/share/man/man1/samtools-flagstat.1.gz
-rw-r--r-- root/root 2171 2024-02-17 17:22 ./usr/share/man/man1/samtools-fqidx.1.gz
-rw-r--r-- root/root 1336 2024-02-17 17:22 ./usr/share/man/man1/samtools-head.1.gz
-rw-r--r-- root/root 1415 2024-02-17 17:22 ./usr/share/man/man1/samtools-idxstats.1.gz
-rw-r--r-- root/root 3577 2024-02-17 17:22 ./usr/share/man/man1/samtools-import.1.gz
-rw-r--r-- root/root 1952 2024-02-17 17:22 ./usr/share/man/man1/samtools-index.1.gz
-rw-r--r-- root/root 3906 2024-02-17 17:22 ./usr/share/man/man1/samtools-markdup.1.gz
-rw-r--r-- root/root 3689 2024-02-17 17:22 ./usr/share/man/man1/samtools-merge.1.gz
-rw-r--r-- root/root 7507 2024-02-17 17:22 ./usr/share/man/man1/samtools-mpileup.1.gz
-rw-r--r-- root/root 1439 2024-02-17 17:22 ./usr/share/man/man1/samtools-phase.1.gz
-rw-r--r-- root/root 1681 2024-02-17 17:22 ./usr/share/man/man1/samtools-quickcheck.1.gz
-rw-r--r-- root/root 1881 2024-02-17 17:22 ./usr/share/man/man1/samtools-reference.1.gz
-rw-r--r-- root/root 1966 2024-02-17 17:22 ./usr/share/man/man1/samtools-reheader.1.gz
-rw-r--r-- root/root 2310 2024-02-17 17:22 ./usr/share/man/man1/samtools-reset.1.gz
-rw-r--r-- root/root 1473 2024-02-17 17:22 ./usr/share/man/man1/samtools-rmdup.1.gz
-rw-r--r-- root/root 2283 2024-02-17 17:22 ./usr/share/man/man1/samtools-samples.1.gz
-rw-r--r-- root/root 4725 2024-02-17 17:22 ./usr/share/man/man1/samtools-sort.1.gz
-rw-r--r-- root/root 2581 2024-02-17 17:22 ./usr/share/man/man1/samtools-split.1.gz
-rw-r--r-- root/root 6569 2024-02-17 17:22 ./usr/share/man/man1/samtools-stats.1.gz
-rw-r--r-- root/root 1430 2024-02-17 17:22 ./usr/share/man/man1/samtools-targetcut.1.gz
-rw-r--r-- root/root 2048 2024-02-17 17:22 ./usr/share/man/man1/samtools-tview.1.gz
-rw-r--r-- root/root 7194 2024-02-17 17:22 ./usr/share/man/man1/samtools-view.1.gz
-rw-r--r-- root/root 15961 2024-02-17 17:22 ./usr/share/man/man1/samtools.1.gz
-rw-r--r-- root/root 410 2024-02-17 17:22 ./usr/share/man/man1/samtools.pl.1.gz
-rw-r--r-- root/root 518 2024-02-17 17:22 ./usr/share/man/man1/wgsim.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 30212
Build-Time: 288
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 446
Job: samtools_1.19.2-1
Machine Architecture: armhf
Package: samtools
Package-Time: 771
Source-Version: 1.19.2-1
Space: 30212
Status: successful
Version: 1.19.2-1
--------------------------------------------------------------------------------
Finished at 2024-02-20T06:08:16Z
Build needed 00:12:51, 30212k disk space