[med-svn] samtools 01/01: Build logs for samtools_1.0-1~experimental_amd64.changes.
Charles Plessy
plessy at moszumanska.debian.org
Sun Aug 24 07:22:53 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch debian/logs/experimental
in repository samtools.
commit 1aec5b74f0b703b71928ec6b9b4d9dcb3a78251c
Author: Charles Plessy <plessy at debian.org>
Date: Sun Aug 24 16:20:05 2014 +0900
Build logs for samtools_1.0-1~experimental_amd64.changes.
---
amd64.changes | 132 ++--
amd64.log | 2215 ++++++++++++++++++++++++++++++++++-----------------------
dsc | 66 +-
upload | 14 +-
4 files changed, 1448 insertions(+), 979 deletions(-)
diff --git a/amd64.changes b/amd64.changes
index aa894c6..fc20c8e 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -1,68 +1,90 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
+Date: Sat, 23 Aug 2014 16:02:12 +0900
Source: samtools
-Binary: samtools libbam-dev
-Architecture: source amd64
-Version: 0.1.19-1
-Distribution: unstable
+Binary: samtools samtools-test
+Architecture: source amd64 all
+Version: 1.0-1~experimental
+Distribution: experimental
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
+Description:
samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
+ samtools-test - test files for the samtools package.
+Closes: 544976
+Changes:
+ samtools (1.0-1~experimental) experimental; urgency=low
.
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
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- 3a5880dd0940e98447caa70799b76a39091d3b38 557812 samtools_0.1.19.orig.tar.gz
- 4e18f7699ba4c4cf5ac9503b3bab1f017731414b 10215 samtools_0.1.19-1.debian.tar.gz
- d65798025fa3a03cc2366e0b6bf75a6fc35d48a4 562956 samtools_0.1.19-1_amd64.deb
- 8c400aca23a6ca41b36e6884665939abfd8f9352 123276 libbam-dev_0.1.19-1_amd64.deb
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- f1da7fbdc6956b7aa68dd9cad7435f1ccdc6f6601309761f3845e3a1327da77e 123276 libbam-dev_0.1.19-1_amd64.deb
-Files:
- c239aee949f239c0cb7c9329039eb827 2078 science optional samtools_0.1.19-1.dsc
- 1229dc88487a49b03e69a5c0aa2f8a1e 557812 science optional samtools_0.1.19.orig.tar.gz
- 467846afb2de05547f0ffed136290f8d 10215 science optional samtools_0.1.19-1.debian.tar.gz
- 5195be37dd92ae9c7f2657eacdd40ba2 562956 science optional samtools_0.1.19-1_amd64.deb
- 20ba2fee341db9e3659bce6165aa6763 123276 libdevel optional libbam-dev_0.1.19-1_amd64.deb
+ 54ca0c1 Merge with upstream's develop branch.
+ 241a731 razip was removed from samtools.
+ dc25b81 debian/watch: also track release candidates.
+ 07aaf71 Indicate repository layout in git-buildpackage conf. file.
+ .
+ * debian/control
+ .
+ 8bc0fb7 Stop depending on CDBS and quilt.
+ e613142 Drop static libbam, replaced by the dynamic libhts (Closes: #544976).
+ b5f284c Build-depend on tabix for the regression tests, that use bgzip.
+ 9febad6 Recommend python since samtools installs a python script in /usr/bin.
+ e6ad97f Conforms to Policy 3.9.5.
+ .
+ * New package samtools-test
+ .
+ 7293cca Create a test package for the test data.
+ 6bd7b89 Adjust install file for two-package build.
+ caff5f5 Clean before installing test files (this removes compiled files).
+ .
+ * debian/rules
+ .
+ c930cbb Use Debhelper instead of CDBS and rely on the new upstream Makefile.
+ 845581d Adjust for dynamic linking.
+ d859052 Indicate path to packaged bgzip.
+ cb23517 Mimick Makefile's CPPFLAGS.
+ aee1c6c Allow parallel building.
+ .
+ * debian/patches
+ .
+ f73d764 d062687 Refreshed patches.
+ 2c52f6a 61ac2c5 Forwarded patches on GitHub.
+ b8eb378 Dropped fix_example_makefile.patch, obsolete.
+ 66079b9 Correct path to python interpreter.
+ 218c1c1 Modify Makefile to facilitate dynamic linking.
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+Files:
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+ 7d0546cd0f64d1e6abc04f43aee689bb 2635142 science optional samtools-test_1.0-1~experimental_all.deb
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diff --git a/amd64.log b/amd64.log
index 72f115a..bd51522 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,887 +1,1334 @@
-sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on aqwa.igloo
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (amd64) 30 mars 2013 17:33 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Distribution: unstable
-Machine Architecture: amd64
-Host Architecture: amd64
-Build Architecture: amd64
-
-I: NOTICE: Log filtering will replace 'build/samtools-oC2Dff/samtools-0.1.19' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-oC2Dff' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-b13f39f8-12b1-4b0f-aa4e-3621693a5063' with '«CHROOT»'
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Update chroot │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Hit ftp://ftp.jp.debian.org sid Release.gpg
-Hit ftp://ftp.jp.debian.org sid Release
-Hit ftp://ftp.jp.debian.org sid/main Sources/DiffIndex
-Hit ftp://ftp.jp.debian.org sid/main amd64 Packages/DiffIndex
-Hit ftp://ftp.jp.debian.org sid/main Translation-en/DiffIndex
-Reading package lists...
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Local sources
-─────────────
-
-samtools_0.1.19-1.dsc exists in .; copying to chroot
-
-Check arch
-──────────
-
-Merged Build-Depends: build-essential, fakeroot
-Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-5mJlIc/apt_archive/sbuild-build-depends-core-dummy.deb'.
-OK
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (apt-based resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
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-Installing build dependencies
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-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-cjyhAe/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
-OK
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (apt-based resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Installing build dependencies
-Reading package lists...
-Building dependency tree...
-Reading state information...
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-Selecting previously unselected package libunistring0:amd64.
-Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ...
-Selecting previously unselected package libgettextpo0:amd64.
-Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-10_amd64.deb) ...
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-Selecting previously unselected package libasprintf-dev:amd64.
-Unpacking libasprintf-dev:amd64 (from .../libasprintf-dev_0.18.1.1-10_amd64.deb) ...
-Selecting previously unselected package libgettextpo-dev:amd64.
-Unpacking libgettextpo-dev:amd64 (from .../libgettextpo-dev_0.18.1.1-10_amd64.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_amd64.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_amd64.deb) ...
-Selecting previously unselected package libtinfo-dev:amd64.
-Unpacking libtinfo-dev:amd64 (from .../libtinfo-dev_5.9-10_amd64.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_amd64.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev:amd64.
-Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_amd64.deb) ...
-Selecting previously unselected package sbuild-build-depends-samtools-dummy.
-Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
-Setting up libpipeline1:amd64 (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:amd64 (0.18.1.1-10) ...
-Setting up libmagic1:amd64 (1:5.11-2.1) ...
-Setting up libpcre3:amd64 (1:8.31-2) ...
-Setting up libxml2:amd64 (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:amd64 (3.0.10-3) ...
-Setting up libglib2.0-0:amd64 (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:amd64 (0.6.6-2) ...
-Setting up libunistring0:amd64 (0.9.3-5) ...
-Setting up libgettextpo0:amd64 (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:amd64 (0.18.1.1-10) ...
-Setting up libgettextpo-dev:amd64 (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:amd64 (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build environment │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Kernel: Linux 3.2.0-4-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.7_4.7.2-5 gcc-4.7_4.7.2-5 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5 linux-libc-dev_3.2.41-2
-Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-5 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42. [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-dpkg-source: warning: extracting unsigned source package (samtools_0.1.19-1.dsc)
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-Sufficient free space for build
-
-User Environment
-────────────────
-
-HOME=/sbuild-nonexistent
-LOGNAME=charles
-PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-SCHROOT_ALIAS_NAME=unstable
-SCHROOT_CHROOT_NAME=sid-amd64-sbuild
-SCHROOT_COMMAND=env
-SCHROOT_GID=1000
-SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-b13f39f8-12b1-4b0f-aa4e-3621693a5063
-SCHROOT_UID=1000
-SCHROOT_USER=charles
-SHELL=/bin/sh
-TERM=xterm
-USER=charles
-USERNAME=charles
-XDG_RUNTIME_DIR=/run/user/charles
-XDG_SEAT=seat0
-XDG_SESSION_ID=2
-XDG_VTNR=7
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
-dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture amd64
+ dpkg-buildpackage -rfakeroot -D -us -uc -i -I -j2
+dpkg-buildpackage: paquet source samtools
+dpkg-buildpackage: version source 1.0-1~experimental
+dpkg-buildpackage: distribution source experimental
+dpkg-buildpackage: source changé par Charles Plessy <plessy at debian.org>
+ dpkg-source -i -I --before-build samtools
+dpkg-buildpackage: architecture hôte amd64
+dpkg-source: info: utilisation des options depuis samtools/debian/source/options : --single-debian-patch
+dpkg-source: info: mise en place de fix_coverage_cap.patch
+dpkg-source: info: mise en place de fix_segfault_with_small_ref.patch
+dpkg-source: info: mise en place de dynamic-build.patch
+dpkg-source: info: mise en place de python-wrong-path-for-interpreter.patch
fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
-make[2]: Entering directory `/«PKGBUILDDIR»/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- dpkg-source -b samtools-0.1.19
-dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: building samtools using existing ./samtools_0.1.19.orig.tar.gz
-dpkg-source: info: building samtools in samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: building samtools in samtools_0.1.19-1.dsc
+dh clean --parallel
+ dh_testdir -O--parallel
+ dh_auto_clean -O--parallel
+ make -j2 distclean
+make[1]: Entering directory '/home/charles/debian/debian-med/samtools'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+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
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header 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
+rm -f TAGS
+make[1]: Leaving directory '/home/charles/debian/debian-med/samtools'
+ dh_clean -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} + \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
+ rm -f *-stamp
+ dpkg-source -i -I -b samtools
+dpkg-source: info: utilisation des options depuis samtools/debian/source/options : --single-debian-patch
+dpkg-source: info: utilisation du format source « 3.0 (quilt) »
+dpkg-source: info: construction de samtools en utilisant le ./samtools_1.0.orig.tar.gz existant
+dpkg-source: info: modifications locales détectées, les fichiers modifiés sont :
+ samtools/.travis.yml
+ samtools/README.md
+dpkg-source: info: les modifications locales ont été enregistrées dans un nouveau patch: samtools/debian/patches/debian-changes
+dpkg-source: info: construction de samtools dans samtools_1.0-1~experimental.debian.tar.xz
+dpkg-source: info: construction de samtools dans samtools_1.0-1~experimental.dsc
debian/rules build
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-File series fully applied, ends at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
-make[2]: Entering directory `/«PKGBUILDDIR»/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/«PKGBUILDDIR»'
-make[3]: Entering directory `/«PKGBUILDDIR»'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«PKGBUILDDIR»'
-make[3]: Entering directory `/«PKGBUILDDIR»/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«PKGBUILDDIR»/bcftools'
-make[3]: Entering directory `/«PKGBUILDDIR»/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«PKGBUILDDIR»/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
-make[2]: Entering directory `/«PKGBUILDDIR»/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-md5.c: In function 'MD5Final':
-md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-md5.c: In function 'MD5Final':
-md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/«PKGBUILDDIR»/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/«PKGBUILDDIR»/examples'
-touch debian/stamp-makefile-check
+dh build --parallel
+ dh_testdir -O--parallel
+ dh_auto_configure -O--parallel
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/home/charles/debian/debian-med/samtools'
+dh_auto_build -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a \
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
+ LDLIBS="-lhts"
+ make -j2 HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+make[2]: Entering directory '/home/charles/debian/debian-med/samtools'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.0-148-g5e83465-dirty"' > version.h
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.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 libbam.a /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lcurse [...]
+make[2]: Leaving directory '/home/charles/debian/debian-med/samtools'
+make[1]: Leaving directory '/home/charles/debian/debian-med/samtools'
+ debian/rules override_dh_auto_test
+make[1]: Entering directory '/home/charles/debian/debian-med/samtools'
+dh_auto_test -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a \
+ BGZIP=/usr/bin/bgzip
+ make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+make[2]: Entering directory '/home/charles/debian/debian-med/samtools'
+test/test.pl --exec bgzip=/usr/bin/bgzip
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/Ol_soa6wzr/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/Ol_soa6wzr/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/Ol_soa6wzr/bgzip.dat.gz
+.. ok
+
+/home/charles/debian/debian-med/samtools/samtools faidx /tmp/Ol_soa6wzr/faidx.fa 3:11-13 | grep -v '^>'
+.. ok
+
+/home/charles/debian/debian-med/samtools/samtools faidx /tmp/Ol_soa6wzr/faidx.fa.gz 3:11-13 | grep -v '^>'
+.. ok
+
+/home/charles/debian/debian-med/samtools/samtools faidx /tmp/Ol_soa6wzr/faidx.fa 2:998-1003 | grep -v '^>'
+.. ok
+
+/home/charles/debian/debian-med/samtools/samtools faidx /tmp/Ol_soa6wzr/faidx.fa.gz 2:998-1003 | grep -v '^>'
+.. ok
+
+/home/charles/debian/debian-med/samtools/samtools faidx /tmp/Ol_soa6wzr/faidx.fa 1:100-104 | grep -v '^>'
+.. ok
+
+/home/charles/debian/debian-med/samtools/samtools faidx /tmp/Ol_soa6wzr/faidx.fa.gz 1:100-104 | grep -v '^>'
+.. ok
+
+/home/charles/debian/debian-med/samtools/samtools faidx /tmp/Ol_soa6wzr/faidx.fa 1:99998-100007 | grep -v '^>'
+.. ok
+
+/home/charles/debian/debian-med/samtools/samtools faidx /tmp/Ol_soa6wzr/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
+
+test_index:
+ /home/charles/debian/debian-med/samtools/samtools index /tmp/Ol_soa6wzr/large_chrom.bam
+
+.. expected failure
+
+test_index:
+ /home/charles/debian/debian-med/samtools/samtools view /tmp/Ol_soa6wzr/large_chrom.bam ref2
+
+ The outputs stdout differ:
+ /home/charles/debian/debian-med/samtools/test/dat/large_chrom.out
+ /home/charles/debian/debian-med/samtools/test/dat/large_chrom.out.new
+.. expected failure
+
+test_index:
+ /home/charles/debian/debian-med/samtools/samtools view /tmp/Ol_soa6wzr/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_mpileup:
+ /home/charles/debian/debian-med/samtools/samtools mpileup -b /tmp/Ol_soa6wzr/mpileup.bam.list -f /tmp/Ol_soa6wzr/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /home/charles/debian/debian-med/samtools/samtools mpileup -b /tmp/Ol_soa6wzr/mpileup.cram.list -f /tmp/Ol_soa6wzr/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /home/charles/debian/debian-med/samtools/samtools mpileup -uvDV -b /tmp/Ol_soa6wzr/mpileup.bam.list -f /tmp/Ol_soa6wzr/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /home/charles/debian/debian-med/samtools/samtools mpileup -uvDV -b /tmp/Ol_soa6wzr/mpileup.cram.list -f /tmp/Ol_soa6wzr/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /home/charles/debian/debian-med/samtools/samtools mpileup -B --ff 0x14 -f /tmp/Ol_soa6wzr/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Ol_soa6wzr/mpileup.1.bam | grep -v mpileup
+.. ok
+
+test_mpileup:
+ /home/charles/debian/debian-med/samtools/samtools mpileup -B --ff 0x14 -f /tmp/Ol_soa6wzr/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Ol_soa6wzr/mpileup.1.cram | grep -v mpileup
+.. ok
+
+test_usage:
+ samtools
+ samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+.. ok
+
+test_usage_subcommand:
+ samtools faidx
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+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 rmdup
+
+ 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 bamshuf
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools cat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools merge
+.. ok
+
+test_usage_subcommand:
+ samtools mpileup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools sort
+.. ok
+
+test_usage_subcommand:
+ samtools split
+.. ok
+
+test_usage_subcommand:
+ samtools bam2fq
+.. ok
+
+test_usage_subcommand:
+ samtools bedcov
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools depth
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools flagstat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools idxstats
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools phase
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools stats
+.. ok
+
+test_usage_subcommand:
+ samtools flags
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools tview
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools view
+
+ 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/Ol_soa6wzr/view.001.fogn (SAM input) .. ok
+
+ 50: Count -R /tmp/Ol_soa6wzr/view.001.fogn (SAM input) .. ok
+
+ 51: Filter -R /tmp/Ol_soa6wzr/view.001.fogn (BAM input) .. ok
+
+ 52: Count -R /tmp/Ol_soa6wzr/view.001.fogn (BAM input) .. ok
+
+ 53: Filter -R /tmp/Ol_soa6wzr/view.001.fogn (CRAM input) .. ok
+
+ 54: Count -R /tmp/Ol_soa6wzr/view.001.fogn (CRAM input) .. ok
+
+ 55: Filter -R /tmp/Ol_soa6wzr/view.001.fogn -r grp2 (SAM input).. ok
+
+ 56: Count -R /tmp/Ol_soa6wzr/view.001.fogn -r grp2 (SAM input).. ok
+
+ 57: Filter -R /tmp/Ol_soa6wzr/view.001.fogn -r grp2 (BAM input).. ok
+
+ 58: Count -R /tmp/Ol_soa6wzr/view.001.fogn -r grp2 (BAM input).. ok
+
+ 59: Filter -R /tmp/Ol_soa6wzr/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 60: Count -R /tmp/Ol_soa6wzr/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 61: Filter -r grp2 -R /tmp/Ol_soa6wzr/view.001.fogn (SAM input).. ok
+
+ 62: Count -r grp2 -R /tmp/Ol_soa6wzr/view.001.fogn (SAM input).. ok
+
+ 63: Filter -r grp2 -R /tmp/Ol_soa6wzr/view.001.fogn (BAM input).. ok
+
+ 64: Count -r grp2 -R /tmp/Ol_soa6wzr/view.001.fogn (BAM input).. ok
+
+ 65: Filter -r grp2 -R /tmp/Ol_soa6wzr/view.001.fogn (CRAM input).. ok
+
+ 66: Count -r grp2 -R /tmp/Ol_soa6wzr/view.001.fogn (CRAM input).. ok
+
+ 67: Filter -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools view -o /tmp/Ol_soa6wzr/view.test067.sam -h -l Library 2 /tmp/Ol_soa6wzr/view.001.sam
+
+
+.. expected failure
+
+ 68: Count -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools view -c -l Library 2 /tmp/Ol_soa6wzr/view.001.sam
+
+
+.. expected failure
+
+ 69: Filter -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools view -o /tmp/Ol_soa6wzr/view.test069.sam -h -l Library 2 /tmp/Ol_soa6wzr/view.test001.bam
+
+
+.. expected failure
+
+ 70: Count -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools view -c -l Library 2 /tmp/Ol_soa6wzr/view.test001.bam
+
+
+.. expected failure
+
+ 71: Filter -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools view -o /tmp/Ol_soa6wzr/view.test071.sam -h -l Library 2 /tmp/Ol_soa6wzr/view.test006.cram
+
+
+.. expected failure
+
+ 72: Count -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools view -c -l Library 2 /tmp/Ol_soa6wzr/view.test006.cram
+
+
+.. expected failure
+
+ 73: Filter -q 50 (SAM input) .. ok
+
+ 74: Count -q 50 (SAM input) .. ok
+
+ 75: Filter -q 50 (BAM input) .. ok
+
+ 76: Count -q 50 (BAM input) .. ok
+
+ 77: Filter -q 50 (CRAM input) .. ok
+
+ 78: Count -q 50 (CRAM input) .. ok
+
+ 79: Filter -q 99 (SAM input) .. ok
+
+ 80: Count -q 99 (SAM input) .. ok
+
+ 81: Filter -q 99 (BAM input) .. ok
+
+ 82: Count -q 99 (BAM input) .. ok
+
+ 83: Filter -q 99 (CRAM input) .. ok
+
+ 84: Count -q 99 (CRAM input) .. ok
+
+ 85: Filter -q 100 (SAM input) .. ok
+
+ 86: Count -q 100 (SAM input) .. ok
+
+ 87: Filter -q 100 (BAM input) .. ok
+
+ 88: Count -q 100 (BAM input) .. ok
+
+ 89: Filter -q 100 (CRAM input) .. ok
+
+ 90: Count -q 100 (CRAM input) .. ok
+
+ 91: Filter -x fa (SAM input) .. ok
+
+ 92: Count -x fa (SAM input) .. ok
+
+ 93: Filter -x fa (BAM input) .. ok
+
+ 94: Count -x fa (BAM input) .. ok
+
+ 95: Filter -x fa (CRAM input) .. ok
+
+ 96: Count -x fa (CRAM input) .. ok
+
+ 97: Filter -x fa -x ha (SAM input) .. ok
+
+ 98: Count -x fa -x ha (SAM input) .. ok
+
+ 99: Filter -x fa -x ha (BAM input) .. ok
+
+ 100: Count -x fa -x ha (BAM input) .. ok
+
+ 101: Filter -x fa -x ha (CRAM input) .. ok
+
+ 102: Count -x fa -x ha (CRAM input) .. ok
+
+ 103: Filter -x fa -r grp2 (SAM input) .. ok
+
+ 104: Count -x fa -r grp2 (SAM input) .. ok
+
+ 105: Filter -x fa -r grp2 (BAM input) .. ok
+
+ 106: Count -x fa -r grp2 (BAM input) .. ok
+
+ 107: Filter -x fa -r grp2 (CRAM input) .. ok
+
+ 108: Count -x fa -r grp2 (CRAM input) .. ok
+
+ 109: Filter -x RG -r grp2 (SAM input) .. ok
+
+ 110: Count -x RG -r grp2 (SAM input) .. ok
+
+ 111: Filter -x RG -r grp2 (BAM input) .. ok
+
+ 112: Count -x RG -r grp2 (BAM input) .. ok
+
+ 113: Filter -x RG -r grp2 (CRAM input) .. ok
+
+ 114: Count -x RG -r grp2 (CRAM input) .. ok
+
+ 115: Filter -m 10 (SAM input) .. ok
+
+ 116: Count -m 10 (SAM input) .. ok
+
+ 117: Filter -m 10 (BAM input) .. ok
+
+ 118: Count -m 10 (BAM input) .. ok
+
+ 119: Filter -m 10 (CRAM input) .. ok
+
+ 120: Count -m 10 (CRAM input) .. ok
+
+ 121: Filter -m 11 (SAM input) .. ok
+
+ 122: Count -m 11 (SAM input) .. ok
+
+ 123: Filter -m 11 (BAM input) .. ok
+
+ 124: Count -m 11 (BAM input) .. ok
+
+ 125: Filter -m 11 (CRAM input) .. ok
+
+ 126: Count -m 11 (CRAM input) .. ok
+
+ 127: Filter -m 15 (SAM input) .. ok
+
+ 128: Count -m 15 (SAM input) .. ok
+
+ 129: Filter -m 15 (BAM input) .. ok
+
+ 130: Count -m 15 (BAM input) .. ok
+
+ 131: Filter -m 15 (CRAM input) .. ok
+
+ 132: Count -m 15 (CRAM input) .. ok
+
+ 133: Filter -m 16 (SAM input) .. ok
+
+ 134: Count -m 16 (SAM input) .. ok
+
+ 135: Filter -m 16 (BAM input) .. ok
+
+ 136: Count -m 16 (BAM input) .. ok
+
+ 137: Filter -m 16 (CRAM input) .. ok
+
+ 138: Count -m 16 (CRAM input) .. ok
+
+ 139: Filter -Q 2 (SAM input) .. ok
+
+ 140: Count -Q 2 (SAM input) .. ok
+
+ 141: Filter -Q 2 (BAM input) .. ok
+
+ 142: Count -Q 2 (BAM input) .. ok
+
+ 143: Filter -Q 2 (CRAM input) .. ok
+
+ 144: Count -Q 2 (CRAM input) .. ok
+
+ 145: Filter -Q 2147483647 (SAM input) .. ok
+
+ 146: Count -Q 2147483647 (SAM input) .. ok
+
+ 147: Filter -Q 2147483647 (BAM input) .. ok
+
+ 148: Count -Q 2147483647 (BAM input) .. ok
+
+ 149: Filter -Q 2147483647 (CRAM input) .. ok
+
+ 150: Count -Q 2147483647 (CRAM input) .. ok
+
+ 151: 1bp reads file SAM -> BAM -> SAM .. ok
+
+ 152: 1bp reads file SAM -> CRAM -> SAM .. ok
+
+ 152: Region Z (BAM input) .. ok
+
+ 153: Count Z (BAM input) .. ok
+
+ 154: Region Z (CRAM input) .. ok
+
+ 155: Count Z (CRAM input) .. ok
+
+ 156: Region Z:30 (BAM input) .. ok
+
+ 157: Count Z:30 (BAM input) .. ok
+
+ 158: Region Z:30 (CRAM input) .. ok
+
+ 159: Count Z:30 (CRAM input) .. ok
+
+ 160: Region Z:20-40 (BAM input) .. ok
+
+ 161: Count Z:20-40 (BAM input) .. ok
+
+ 162: Region Z:20-40 (CRAM input) .. ok
+
+ 163: Count Z:20-40 (CRAM input) .. ok
+
+ 164: Region ref1 (BAM input) .. ok
+
+ 165: Count ref1 (BAM input) .. ok
+
+ 166: Region ref1 (CRAM input) .. ok
+
+ 167: Count ref1 (CRAM input) .. ok
+
+ 168: Region ref1:15 (BAM input) .. ok
+
+ 169: Count ref1:15 (BAM input) .. ok
+
+ 170: Region ref1:15 (CRAM input) .. ok
+
+ 171: Count ref1:15 (CRAM input) .. ok
+
+ 172: Region ref1:15-45 (BAM input) .. ok
+
+ 173: Count ref1:15-45 (BAM input) .. ok
+
+ 174: Region ref1:15-45 (CRAM input) .. ok
+
+ 175: Count ref1:15-45 (CRAM input) .. ok
+
+ 176: Region ref1:15-45 ref2 (BAM input) .. ok
+
+ 177: Count ref1:15-45 ref2 (BAM input) .. ok
+
+ 178: Region ref1:15-45 ref2 (CRAM input) .. ok
+
+ 179: Count ref1:15-45 ref2 (CRAM input) .. ok
+
+ 180: Region ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 181: Count ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 182: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 183: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 184: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 185: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 186: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 187: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 188: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 189: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 190: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 191: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 192: Region -f 128 ref1 (BAM input) .. ok
+
+ 193: Count -f 128 ref1 (BAM input) .. ok
+
+ 194: Region -f 128 ref1 (CRAM input) .. ok
+
+ 195: Count -f 128 ref1 (CRAM input) .. ok
+
+ 196: Region -q 50 ref1:15-45 (BAM input) .. ok
+
+ 197: Count -q 50 ref1:15-45 (BAM input) .. ok
+
+ 198: Region -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 199: Count -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 200: Region -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 201: Count -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 202: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 203: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 204: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed (BAM input).. ok
+
+ 205: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed (BAM input).. ok
+
+ 206: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 207: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 208: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.02.bed (BAM input).. ok
+
+ 209: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.02.bed (BAM input).. ok
+
+ 210: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 211: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 212: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed (BAM input).. ok
+
+ 213: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed (BAM input).. ok
+
+ 214: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed (CRAM input).. ok
+
+ 215: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed (CRAM input).. ok
+
+ 216: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.02.bed (BAM input).. ok
+
+ 217: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.02.bed (BAM input).. ok
+
+ 218: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.02.bed (CRAM input).. ok
+
+ 219: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.02.bed (CRAM input).. ok
+
+ 220: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 221: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 222: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 223: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 224: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 225: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 226: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 227: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 228: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 229: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 230: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 231: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 232: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 233: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 234: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 235: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 236: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+
+ 237: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+
+ 238: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+
+ 239: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+
+ 240: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 241: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 242: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 243: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 244: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 245: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 246: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 247: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 248: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 249: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 250: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 251: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 252: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+
+ 253: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+
+ 254: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+
+ 255: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+
+ 256: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 257: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 258: Region -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 259: Count -L /home/charles/debian/debian-med/samtools/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 260: Make BAM with no M5/UR tags .. ok
+
+ 261: Add @SQ with -t (SAM -> SAM) .. ok
+
+ 262: Add @SQ with -T (SAM -> SAM) .. ok
+
+ 263: Add @SQ with -t (BAM -> SAM) .. ok
+
+ 264: Add @SQ with -T (BAM -> SAM) .. ok
+
+ 265: Add @SQ with -t (SAM -> BAM) .. ok
+
+ 266: Add @SQ with -T (SAM -> BAM) .. ok
+
+ 267: Add @SQ with -t (BAM -> BAM) .. ok
+
+ 268: Add @SQ with -T (BAM -> BAM) .. ok
+
+ 269: Add @SQ with -t (SAM -> CRAM) .. ok
+
+ 270: Add @SQ with -T (SAM -> CRAM) .. ok
+
+ 271: Add @SQ with -t (BAM -> CRAM) .. ok
+
+ 272: Add @SQ with -T (BAM -> CRAM) .. ok
+
+ 273: CIGAR B-operator removal .. ok
+
+ 274: Big SAM -> BAM .. ok
+
+ 275: Big SAM -> BAM (2 threads) .. ok
+
+ 276: Big SAM -> BAM (4 threads) .. ok
+
+ 277: Big SAM -> CRAM .. ok
+
+ 278: Big SAM -> CRAM (2 threads) .. ok
+
+ 279: Big SAM -> CRAM (4 threads) .. ok
+
+ 280: Subsample 0.2 (SAM input) ............ ok
+
+ 281: Subsample 0.5 (SAM input) ............ ok
+
+ 282: Subsample 0.8 (SAM input) ............ ok
+
+ 283: Subsample 0.2 (BAM input) ............ ok
+
+ 284: Subsample 0.5 (BAM input) ............ ok
+
+ 285: Subsample 0.8 (BAM input) ............ ok
+
+ 286: Subsample 0.2 (CRAM input) ............ ok
+
+ 287: Subsample 0.5 (CRAM input) ............ ok
+
+ 288: Subsample 0.8 (CRAM input) ............ ok
+
+test_cat:
+ Generating test data file .................. done
+ Generate BAM file #1 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #2 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #3 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #4 .. ok
+
+ 1: cat BAM files .. ok
+
+ 2: cat recompressed BAM files .. ok
+
+ 3: cat BAM files to stdout .. ok
+
+ 4: cat recompressed BAM files to stdout .. ok
+
+ 5: cat BAM files with new header .. ok
+
+ 6: cat recompressed BAM files with new header .. ok
+
+test_bam2fq:
+ Generate BAM file .. ok
+
+ Generate CRAM file .. ok
+
+ 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
+
+ 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
+
+ 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
+
+ 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
+
+ 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
+
+ 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
+
+test_depad:
+ Generate BAM file .. ok
+
+ depad (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools depad -T /home/charles/debian/debian-med/samtools/test/dat/depad.001.fa /home/charles/debian/debian-med/samtools/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+ depad -s (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools depad -T /home/charles/debian/debian-med/samtools/test/dat/depad.001.fa -s /home/charles/debian/debian-med/samtools/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+ depad -u (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools depad -T /home/charles/debian/debian-med/samtools/test/dat/depad.001.fa -u /home/charles/debian/debian-med/samtools/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+ depad -1 (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools depad -T /home/charles/debian/debian-med/samtools/test/dat/depad.001.fa -1 /home/charles/debian/debian-med/samtools/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+ depad (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools depad -T /home/charles/debian/debian-med/samtools/test/dat/depad.001.fa /tmp/Ol_soa6wzr/depad.001p.bam
+
+
+.. expected failure
+
+ depad -s (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools depad -T /home/charles/debian/debian-med/samtools/test/dat/depad.001.fa -s /tmp/Ol_soa6wzr/depad.001p.bam
+
+
+.. expected failure
+
+ depad -u (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools depad -T /home/charles/debian/debian-med/samtools/test/dat/depad.001.fa -u /tmp/Ol_soa6wzr/depad.001p.bam
+
+
+.. expected failure
+
+ depad -1 (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /home/charles/debian/debian-med/samtools/samtools depad -T /home/charles/debian/debian-med/samtools/test/dat/depad.001.fa -1 /tmp/Ol_soa6wzr/depad.001p.bam
+
+
+.. expected failure
+
+test_stats:
+ /home/charles/debian/debian-med/samtools/samtools stats -r /home/charles/debian/debian-med/samtools/test/stat/test.fa /home/charles/debian/debian-med/samtools/test/stat/1_map_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /home/charles/debian/debian-med/samtools/samtools stats -r /home/charles/debian/debian-med/samtools/test/stat/test.fa /home/charles/debian/debian-med/samtools/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /home/charles/debian/debian-med/samtools/samtools stats -r /home/charles/debian/debian-med/samtools/test/stat/test.fa /home/charles/debian/debian-med/samtools/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /home/charles/debian/debian-med/samtools/samtools stats -r /home/charles/debian/debian-med/samtools/test/stat/test.fa /home/charles/debian/debian-med/samtools/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /home/charles/debian/debian-med/samtools/samtools stats -r /home/charles/debian/debian-med/samtools/test/stat/test.fa /home/charles/debian/debian-med/samtools/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /home/charles/debian/debian-med/samtools/samtools stats -r /home/charles/debian/debian-med/samtools/test/stat/test.fa -i 0 /home/charles/debian/debian-med/samtools/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_merge:
+ /home/charles/debian/debian-med/samtools/samtools merge -s 1 - /home/charles/debian/debian-med/samtools/test/dat/test_input_1_a.sam /home/charles/debian/debian-med/samtools/test/dat/test_input_1_b.sam /home/charles/debian/debian-med/samtools/test/dat/test_input_1_c.sam
+/bin/bash : ligne 1 : 2760 Abandon ( /home/charles/debian/debian-med/samtools/samtools merge -s 1 - /home/charles/debian/debian-med/samtools/test/dat/test_input_1_a.sam /home/charles/debian/debian-med/samtools/test/dat/test_input_1_b.sam /home/charles/debian/debian-med/samtools/test/dat/test_input_1_c.sam ) 2> /tmp/B1_CTGynTr
+
+.. expected failure
+
+test_merge:
+ /home/charles/debian/debian-med/samtools/samtools merge -s 1 - /home/charles/debian/debian-med/samtools/test/dat/test_input_1_a.bam /home/charles/debian/debian-med/samtools/test/dat/test_input_1_b.bam /home/charles/debian/debian-med/samtools/test/dat/test_input_1_c.bam
+.. ok
+
+test_merge:
+ /home/charles/debian/debian-med/samtools/samtools merge -s 1 -b /tmp/YNbZJuYATd - /home/charles/debian/debian-med/samtools/test/dat/test_input_1_a.bam
+.. ok
+
+test_fixmate:
+ /home/charles/debian/debian-med/samtools/samtools fixmate -O sam /home/charles/debian/debian-med/samtools/test/fixmate/1_coord_sort.sam -
+
+.. expected failure
+
+test_fixmate:
+ /home/charles/debian/debian-med/samtools/samtools fixmate -O sam /home/charles/debian/debian-med/samtools/test/fixmate/2_isize_overflow.sam -
+.. ok
+
+test_fixmate:
+ /home/charles/debian/debian-med/samtools/samtools fixmate -O sam /home/charles/debian/debian-med/samtools/test/fixmate/3_reverse_read_pp_lt.sam -
+.. ok
+
+test_fixmate:
+ /home/charles/debian/debian-med/samtools/samtools fixmate -O sam /home/charles/debian/debian-med/samtools/test/fixmate/4_reverse_read_pp_equal.sam -
+.. ok
+
+test_idxstat:
+ /home/charles/debian/debian-med/samtools/samtools idxstats /home/charles/debian/debian-med/samtools/test/dat/test_input_1_a.bam
+.. ok
+
+
+Number of tests:
+ total .. 374
+ passed .. 340
+ failed .. 0
+ expected failure .. 34
+ unexpected pass .. 0
+
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_pretty_header
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+if [ -n "$REF_PATH" ]; then cd test/mpileup && ./regression.sh; fi
+test/split/test_count_rg
+test/split/test_expand_format_string
+test/split/test_filter_header_rg
+test/split/test_parse_args
+make[2]: Leaving directory '/home/charles/debian/debian-med/samtools'
+make[1]: Leaving directory '/home/charles/debian/debian-med/samtools'
fakeroot debian/rules binary
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /«PKGBUILDDIR»/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /«PKGBUILDDIR»/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /«PKGBUILDDIR»/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_amd64.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_amd64.deb'.
- dpkg-genchanges >../samtools_0.1.19-1_amd64.changes
-dpkg-genchanges: including full source code in upload
- dpkg-source --after-build samtools-0.1.19
-dpkg-source: info: unapplying fix_coverage_cap.patch
-dpkg-source: info: unapplying fix_segfault_with_small_ref.patch
-dpkg-source: info: unapplying fix_example_makefile.patch
-dpkg-buildpackage: full upload (original source is included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-1734
-
-Finished
-────────
-
-I: Built successfully
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Changes │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.19-1_amd64.changes:
-────────────────────────────────
-
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: source amd64
-Version: 0.1.19-1
-Distribution: unstable
-Urgency: low
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- 555857290b825846c84a5d760b100ed32e37daad 1192 samtools_0.1.19-1.dsc
- 3a5880dd0940e98447caa70799b76a39091d3b38 557812 samtools_0.1.19.orig.tar.gz
- 4e18f7699ba4c4cf5ac9503b3bab1f017731414b 10215 samtools_0.1.19-1.debian.tar.gz
- d65798025fa3a03cc2366e0b6bf75a6fc35d48a4 562956 samtools_0.1.19-1_amd64.deb
- 8c400aca23a6ca41b36e6884665939abfd8f9352 123276 libbam-dev_0.1.19-1_amd64.deb
-Checksums-Sha256:
- ced6d9d9570dc029b9cf7696c7a4c26aa1cafadd13f0b068684080da2963990e 1192 samtools_0.1.19-1.dsc
- 180c120a040ec660ebecc30ebae664772c0fd503e028173ab2496379bc208c17 557812 samtools_0.1.19.orig.tar.gz
- 980683591cb084f5f825baeffb3c7f08acf01a1a13b8f41e3770b3ee731190a3 10215 samtools_0.1.19-1.debian.tar.gz
- 57c5fcabea54e62e2c666ee303568c4849921ddcd39c5be92530f1081387dc5c 562956 samtools_0.1.19-1_amd64.deb
- f1da7fbdc6956b7aa68dd9cad7435f1ccdc6f6601309761f3845e3a1327da77e 123276 libbam-dev_0.1.19-1_amd64.deb
-Files:
- 285180fb595f6721c8db14fe3726d20d 1192 science optional samtools_0.1.19-1.dsc
- 1229dc88487a49b03e69a5c0aa2f8a1e 557812 science optional samtools_0.1.19.orig.tar.gz
- 467846afb2de05547f0ffed136290f8d 10215 science optional samtools_0.1.19-1.debian.tar.gz
- 5195be37dd92ae9c7f2657eacdd40ba2 562956 science optional samtools_0.1.19-1_amd64.deb
- 20ba2fee341db9e3659bce6165aa6763 123276 libdevel optional libbam-dev_0.1.19-1_amd64.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.19-1_amd64.deb
-───────────────────────────
-
- new debian package, version 2.0.
- size 562956 bytes: control archive=1928 bytes.
- 32 bytes, 1 lines conffiles
- 792 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: amd64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1262
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: processing sequence alignments in SAM and BAM formats
- Samtools is a set of utilities that manipulate nucleotide sequence alignments
- in the binary BAM format. It imports from and exports to the ascii SAM
- (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- to retrieve reads in any regions swiftly. It is designed to work on a stream,
- and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-27 06:52 ./etc/bash_completion.d/samtools
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/lib/samtools/
--rwxr-xr-x root/root 18680 2013-03-30 17:34 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 22696 2013-03-30 17:34 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 172720 2013-03-30 17:34 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 10368 2013-03-30 17:34 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 10368 2013-03-30 17:34 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 14472 2013-03-30 17:34 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 10320 2013-03-30 17:34 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/bin/
--rwxr-xr-x root/root 154664 2013-03-30 17:34 ./usr/bin/bcftools
--rwxr-xr-x root/root 27032 2013-03-30 17:34 ./usr/bin/razip
--rwxr-xr-x root/root 416672 2013-03-30 17:34 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2013-03-30 17:34 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 29649 2013-03-18 23:43 ./usr/share/samtools/plot-bamcheck
--rwxr-xr-x root/root 21028 2013-03-18 23:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 2685 2013-03-18 23:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 2397 2013-03-18 23:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2729 2013-03-18 23:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2696 2013-03-18 23:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 14299 2013-03-18 23:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 7881 2013-03-18 23:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2022 2013-03-18 23:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5989 2013-03-18 23:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 4996 2013-03-18 23:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 18572 2013-03-18 23:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2112 2013-03-18 23:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2415 2013-03-18 23:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 15707 2013-03-18 23:43 ./usr/share/samtools/vcfutils.pl
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2013-03-30 17:34 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 10654 2013-03-30 17:34 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/doc/samtools/
--rw-r--r-- root/root 10421 2013-03-18 23:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 17:32 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 10421 2013-03-18 23:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2013-03-30 17:34 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 786 2013-03-18 23:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2013-03-18 23:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 886 2013-03-18 23:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 114565 2013-03-18 23:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2013-03-18 23:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126580 2013-03-30 17:34 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 5012 2013-03-30 16:03 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2012-01-09 11:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2012-01-09 11:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 916 2013-03-18 23:43 ./usr/share/doc/samtools/AUTHORS
-lrwxrwxrwx root/root 0 2013-03-30 17:34 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_amd64.deb
-─────────────────────────────
-
- new debian package, version 2.0.
- size 123276 bytes: control archive=923 bytes.
- 712 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: amd64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 404
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/include/samtools/
--rw-r--r-- root/root 2688 2013-03-18 23:43 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 3188 2013-03-18 23:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 17815 2013-03-18 23:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 6326 2013-03-18 23:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 25788 2013-03-18 23:43 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/lib/
--rw-r--r-- root/root 327050 2013-03-30 17:34 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 17:34 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 10421 2013-03-18 23:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 17:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 10421 2013-03-18 23:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5012 2013-03-30 16:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 916 2013-03-18 23:43 ./usr/share/doc/libbam-dev/AUTHORS
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-lintian
-───────
-
-P: samtools source: unneeded-build-dep-on-quilt
-W: samtools: duplicate-changelog-files usr/share/doc/samtools/NEWS.gz usr/share/doc/samtools/changelog.gz
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:9
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:23
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:25
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:33
-I: samtools: spelling-error-in-manpage usr/share/man/man1/samtools.1.gz allows to allows one to
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:58
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:59
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:108
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:322
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:346
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:356
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz 30 more occurrences not shown
-W: samtools: unusual-interpreter usr/share/samtools/r2plot.lua #!luajit
-W: samtools: unusual-interpreter usr/share/samtools/vcfutils.lua #!luajit
-W: libbam-dev: duplicate-changelog-files usr/share/doc/libbam-dev/NEWS.gz usr/share/doc/libbam-dev/changelog.gz
-
-I: Lintian run was successful.
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Cleanup │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /«BUILDDIR»
-Not cleaning session: cloned chroot in use
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build Architecture: amd64
-Build-Space: 16868
-Build-Time: 50
-Distribution: unstable
-Host Architecture: amd64
-Install-Time: 34
-Job: samtools_0.1.19-1.dsc
-Lintian: pass
-Machine Architecture: amd64
-Package: samtools
-Package-Time: 89
-Source-Version: 0.1.19-1
-Space: 16868
-Status: successful
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-1734
-Build needed 00:01:29, 16868k disc space
+dh binary --parallel
+ dh_testroot -O--parallel
+ dh_prep -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ debian/rules override_dh_auto_install
+make[1]: Entering directory '/home/charles/debian/debian-med/samtools'
+dh_auto_install -- \
+ prefix=/usr \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a
+ install -d debian/samtools
+ install -d debian/samtools-test
+ make -j2 install DESTDIR=/home/charles/debian/debian-med/samtools/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a
+make[2]: Entering directory '/home/charles/debian/debian-med/samtools'
+mkdir -p -m 755 /home/charles/debian/debian-med/samtools/debian/tmp/usr/bin /home/charles/debian/debian-med/samtools/debian/tmp/usr/share/man/man1
+install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /home/charles/debian/debian-med/samtools/debian/tmp/usr/bin
+install -p -m 644 samtools.1 /home/charles/debian/debian-med/samtools/debian/tmp/usr/share/man/man1
+make[2]: Leaving directory '/home/charles/debian/debian-med/samtools'
+make clean
+make[2]: Entering directory '/home/charles/debian/debian-med/samtools'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+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
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header 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
+make[2]: Leaving directory '/home/charles/debian/debian-med/samtools'
+make[1]: Leaving directory '/home/charles/debian/debian-med/samtools'
+ dh_install -O--parallel
+ install -d debian/samtools//usr
+ cp -a debian/tmp/usr/bin debian/samtools//usr/
+ install -d debian/samtools//usr/share/man
+ cp -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
+ install -d debian/samtools-test/usr/share/samtools
+ cp -a ./test debian/samtools-test/usr/share/samtools/
+ dh_installdocs -O--parallel
+ install -g 0 -o 0 -d debian/samtools/usr/share/doc/samtools
+ cp -a AUTHORS debian/samtools/usr/share/doc/samtools
+ cp -a debian/reference debian/samtools/usr/share/doc/samtools
+ chown -R 0:0 debian/samtools/usr/share/doc
+ chmod -R go=rX debian/samtools/usr/share/doc
+ chmod -R u\+rw debian/samtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/samtools/usr/share/doc/samtools/copyright
+ install -g 0 -o 0 -d debian/samtools-test/usr/share/doc/samtools-test
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/samtools-test/usr/share/doc/samtools-test/copyright
+ dh_installchangelogs -O--parallel
+ install -o 0 -g 0 -p -m644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 debian/changelog debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian
+ dh_installman -O--parallel
+ man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
+ chmod 644 samtools.1.new
+ mv -f samtools.1.new samtools.1
+ dh_perl -O--parallel
+ (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
+ mv debian/samtools.substvars.new debian/samtools.substvars
+ (grep -s -v perl:Depends debian/samtools-test.substvars; echo perl:Depends=perl) > debian/samtools-test.substvars.new
+ mv debian/samtools-test.substvars.new debian/samtools-test.substvars
+ dh_link -O--parallel
+ dh_compress -O--parallel
+ cd debian/samtools
+ chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ cd '/home/charles/debian/debian-med/samtools'
+ cd debian/samtools-test
+ chmod a-x usr/share/doc/samtools-test/changelog.Debian
+ gzip -9nf usr/share/doc/samtools-test/changelog.Debian
+ cd '/home/charles/debian/debian-med/samtools'
+ dh_fixperms -O--parallel
+ find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/samtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/samtools/usr/share/doc -type f ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/samtools/usr/share/man debian/samtools/usr/man/ debian/samtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools/usr/lib/perl5 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/samtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
+ find debian/samtools-test -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/samtools-test ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/samtools-test/usr/share/doc -type f ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/samtools-test/usr/share/man debian/samtools-test/usr/man/ debian/samtools-test/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test/usr/lib/perl5 debian/samtools-test/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools-test/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
+ dh_strip -O--parallel
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ dh_makeshlibs -O--parallel
+ rm -f debian/samtools/DEBIAN/shlibs
+ rm -f debian/samtools-test/DEBIAN/shlibs
+ dh_shlibdeps -O--parallel
+ install -o 0 -g 0 -d debian/samtools/DEBIAN
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short
+dpkg-shlibdeps: avertissement: la dépendance pourrait être évitée si « debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools » n'y étaient pas lié avec libhts.so.1 sans nécessité (ils n'utilisent aucun des symboles de la bibliothèque).
+ install -o 0 -g 0 -d debian/samtools-test/DEBIAN
+ dh_installdeb -O--parallel
+ dh_gencontrol -O--parallel
+ echo misc:Depends= >> debian/samtools.substvars
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
+dpkg-gencontrol: avertissement: paquet samtools : variable de substitution inutilisée ${perl:Depends}
+ chmod 644 debian/samtools/DEBIAN/control
+ chown 0:0 debian/samtools/DEBIAN/control
+ echo misc:Depends= >> debian/samtools-test.substvars
+ dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -Pdebian/samtools-test
+dpkg-gencontrol: avertissement: paquet samtools-test : variable de substitution inutilisée ${perl:Depends}
+ chmod 644 debian/samtools-test/DEBIAN/control
+ chown 0:0 debian/samtools-test/DEBIAN/control
+ dh_md5sums -O--parallel
+ (cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/samtools/DEBIAN/md5sums
+ chown 0:0 debian/samtools/DEBIAN/md5sums
+ (cd debian/samtools-test >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/samtools-test/DEBIAN/md5sums
+ chown 0:0 debian/samtools-test/DEBIAN/md5sums
+ dh_builddeb -O--parallel
+ dpkg-deb --build debian/samtools ..
+ dpkg-deb --build debian/samtools-test ..
+dpkg-deb : construction du paquet « samtools-test » dans « ../samtools-test_1.0-1~experimental_all.deb ».
+dpkg-deb : construction du paquet « samtools » dans « ../samtools_1.0-1~experimental_amd64.deb ».
+ dpkg-genchanges >../samtools_1.0-1~experimental_amd64.changes
+dpkg-genchanges: inclusion du code source original dans l'envoi (« upload »)
+ dpkg-source -i -I --after-build samtools
+dpkg-source: info: utilisation des options depuis samtools/debian/source/options : --single-debian-patch
+dpkg-source: info: retrait de debian-changes
+dpkg-source: info: retrait de python-wrong-path-for-interpreter.patch
+dpkg-source: info: retrait de dynamic-build.patch
+dpkg-source: info: retrait de fix_segfault_with_small_ref.patch
+dpkg-source: info: retrait de fix_coverage_cap.patch
+dpkg-buildpackage: envoi complet (inclusion du code source d'origine)
+Now running lintian...
+W: samtools-test: package-contains-vcs-control-file usr/share/samtools/test/merge/.gitignore
+W: samtools-test: package-contains-vcs-control-file usr/share/samtools/test/mpileup/.gitignore
+W: samtools-test: package-contains-vcs-control-file usr/share/samtools/test/split/.gitignore
+W: samtools-test: executable-not-elf-or-script usr/share/samtools/test/mpileup/bcf_filter.sh
+W: samtools: script-with-language-extension usr/bin/blast2sam.pl
+W: samtools: script-with-language-extension usr/bin/bowtie2sam.pl
+W: samtools: script-with-language-extension usr/bin/export2sam.pl
+W: samtools: script-with-language-extension usr/bin/interpolate_sam.pl
+W: samtools: script-with-language-extension usr/bin/novo2sam.pl
+W: samtools: script-with-language-extension usr/bin/psl2sam.pl
+W: samtools: script-with-language-extension usr/bin/sam2vcf.pl
+W: samtools: script-with-language-extension usr/bin/samtools.pl
+W: samtools: script-with-language-extension usr/bin/seq_cache_populate.pl
+W: samtools: script-with-language-extension usr/bin/soap2sam.pl
+W: samtools: script-with-language-extension usr/bin/varfilter.py
+W: samtools: script-with-language-extension usr/bin/wgsim_eval.pl
+W: samtools: script-with-language-extension usr/bin/zoom2sam.pl
+W: samtools: binary-without-manpage usr/bin/ace2sam
+W: samtools: binary-without-manpage usr/bin/blast2sam.pl
+W: samtools: binary-without-manpage usr/bin/bowtie2sam.pl
+W: samtools: binary-without-manpage usr/bin/export2sam.pl
+W: samtools: binary-without-manpage usr/bin/interpolate_sam.pl
+W: samtools: binary-without-manpage usr/bin/maq2sam-long
+W: samtools: binary-without-manpage usr/bin/maq2sam-short
+W: samtools: binary-without-manpage usr/bin/md5fa
+W: samtools: binary-without-manpage usr/bin/md5sum-lite
+W: samtools: binary-without-manpage usr/bin/novo2sam.pl
+W: samtools: binary-without-manpage usr/bin/plot-bamstats
+W: samtools: binary-without-manpage usr/bin/psl2sam.pl
+W: samtools: binary-without-manpage usr/bin/sam2vcf.pl
+W: samtools: binary-without-manpage usr/bin/samtools.pl
+W: samtools: binary-without-manpage usr/bin/seq_cache_populate.pl
+W: samtools: binary-without-manpage usr/bin/soap2sam.pl
+W: samtools: binary-without-manpage usr/bin/varfilter.py
+W: samtools: binary-without-manpage usr/bin/wgsim
+W: samtools: binary-without-manpage usr/bin/wgsim_eval.pl
+W: samtools: binary-without-manpage usr/bin/zoom2sam.pl
+Finished running lintian.
diff --git a/dsc b/dsc
index 7adef0c..1883d9c 100644
--- a/dsc
+++ b/dsc
@@ -1,45 +1,45 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
Format: 3.0 (quilt)
Source: samtools
-Binary: samtools, libbam-dev
-Architecture: any
-Version: 0.1.19-1
+Binary: samtools, samtools-test
+Architecture: any all
+Version: 1.0-1~experimental
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>, Dominique Belhachemi <domibel at debian.org>
-Homepage: http://samtools.sourceforge.net
-Standards-Version: 3.9.4
+Homepage: http://www.htslib.org/
+Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/samtools.git
Vcs-Git: git://anonscm.debian.org/debian-med/samtools.git
-Build-Depends: debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Package-List:
- libbam-dev deb libdevel optional
- samtools deb science optional
-Checksums-Sha1:
- 3a5880dd0940e98447caa70799b76a39091d3b38 557812 samtools_0.1.19.orig.tar.gz
- 4e18f7699ba4c4cf5ac9503b3bab1f017731414b 10215 samtools_0.1.19-1.debian.tar.gz
-Checksums-Sha256:
- 180c120a040ec660ebecc30ebae664772c0fd503e028173ab2496379bc208c17 557812 samtools_0.1.19.orig.tar.gz
- 980683591cb084f5f825baeffb3c7f08acf01a1a13b8f41e3770b3ee731190a3 10215 samtools_0.1.19-1.debian.tar.gz
-Files:
- 1229dc88487a49b03e69a5c0aa2f8a1e 557812 samtools_0.1.19.orig.tar.gz
- 467846afb2de05547f0ffed136290f8d 10215 samtools_0.1.19-1.debian.tar.gz
+Build-Depends: debhelper (>= 9), bash-completion, libncurses5-dev, zlib1g-dev, tabix (>= 1.0)
+Package-List:
+ samtools deb science optional arch=any
+ samtools-test deb science optional arch=all
+Checksums-Sha1:
+ 78bdac301a2a342a2cfac100b79fb5fa99808114 4291657 samtools_1.0.orig.tar.gz
+ 35c173f001cd8ebdfa9cc600592412ec57bf3147 9484 samtools_1.0-1~experimental.debian.tar.xz
+Checksums-Sha256:
+ c9be4ca074d9645f2782394c95366040f6d2e7334b513968fa8fb26460b626fe 4291657 samtools_1.0.orig.tar.gz
+ 6b6f16308a59e2ebb59c8456ccc6956e270517ed9d3a20c9b1dc74890676fff3 9484 samtools_1.0-1~experimental.debian.tar.xz
+Files:
+ 7eff9d605f21b0910887424069bae72e 4291657 samtools_1.0.orig.tar.gz
+ fd9650c920941de1547b02c62540aacd 9484 samtools_1.0-1~experimental.debian.tar.xz
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-Version: GnuPG v1.4.12 (GNU/Linux)
+Version: GnuPG v1
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diff --git a/upload b/upload
index 4a9e718..d52a025 100644
--- a/upload
+++ b/upload
@@ -1,7 +1,7 @@
-u samtools_0.1.19-1.dsc ftp.upload.debian.org Sat Mar 30 17:51:46 2013
-u libbam-dev_0.1.19-1_amd64.deb ftp.upload.debian.org Sat Mar 30 17:51:49 2013
-u samtools_0.1.19-1.debian.tar.gz ftp.upload.debian.org Sat Mar 30 17:51:51 2013
-u samtools_0.1.19.orig.tar.gz ftp.upload.debian.org Sat Mar 30 17:51:57 2013
-u samtools_0.1.19-1_amd64.deb ftp.upload.debian.org Sat Mar 30 17:52:02 2013
-u samtools_0.1.19-1_amd64.changes ftp.upload.debian.org Sat Mar 30 17:52:03 2013
-s samtools_0.1.19-1_amd64.changes ftp.upload.debian.org Sat Mar 30 17:52:03 2013
+u samtools_1.0-1~experimental_amd64.deb ftp.upload.debian.org Sat Aug 23 16:19:06 2014
+u samtools_1.0.orig.tar.gz ftp.upload.debian.org Sat Aug 23 16:19:09 2014
+u samtools-test_1.0-1~experimental_all.deb ftp.upload.debian.org Sat Aug 23 16:19:12 2014
+u samtools_1.0-1~experimental.dsc ftp.upload.debian.org Sat Aug 23 16:19:14 2014
+u samtools_1.0-1~experimental.debian.tar.xz ftp.upload.debian.org Sat Aug 23 16:19:15 2014
+u samtools_1.0-1~experimental_amd64.changes ftp.upload.debian.org Sat Aug 23 16:19:17 2014
+s samtools_1.0-1~experimental_amd64.changes ftp.upload.debian.org Sat Aug 23 16:19:17 2014
--
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