[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, meta, updated. meta/0.1.13-1-3-gbb0d984
Charles Plessy
plessy at debian.org
Tue Apr 12 11:02:34 UTC 2011
The following commit has been merged in the meta branch:
commit bb0d984fb10368931db6e16848a2a67c12e3146b
Author: Charles Plessy <plessy at debian.org>
Date: Tue Apr 12 19:58:46 2011 +0900
Uploaded samtools_0.1.15-1_amd64.changes.
diff --git a/amd64.changes b/amd64.changes
index c410fc6..c4d4c1c 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,11 +2,11 @@
Hash: SHA256
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: source amd64
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -15,42 +15,45 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- 62df6b20afe456dd9367aa2214b1691cde28d020 1939 samtools_0.1.14-1.dsc
- 03d537ae69afa1607ba3f88a45aaff27d3ba4bd1 370287 samtools_0.1.14.orig.tar.bz2
- 3363682d767cc5aad089f40c49e3c70484da5be2 6869 samtools_0.1.14-1.debian.tar.gz
- cd07ae55e6c70a148ec68e60de7d32ae58adb733 593618 samtools_0.1.14-1_amd64.deb
- 1ad8d4c64330f90a6d3b60cd2a06dce44fa1ef41 165312 libbam-dev_0.1.14-1_amd64.deb
+ 90e920f4a021ecb320f82f7ea748686563096ed1 1939 samtools_0.1.15-1.dsc
+ 0a0f05928ba40ce95d4feda0cd0742ccd1b69e76 374429 samtools_0.1.15.orig.tar.bz2
+ bc8b3ec45fc1bd706858596b68661a654678b46e 7005 samtools_0.1.15-1.debian.tar.gz
+ 4f5a23bdbaa730c3c5e11e4e5792a00c9c0e5d3b 599104 samtools_0.1.15-1_amd64.deb
+ 473799f45bf22dde0d9d89b1a84a3529d1c85840 169002 libbam-dev_0.1.15-1_amd64.deb
Checksums-Sha256:
- bb4e109187e11c57e13237a8d491d108499038d1d9d4dab79e38a86c95b523d2 1939 samtools_0.1.14-1.dsc
- 8bbe8fe4240fe98868891a27093e86ffb3149b716d9659db28c84df0c91d5975 370287 samtools_0.1.14.orig.tar.bz2
- 048f6988bbc21acd19f54e2f42ed105834981220f35a32397c6c202c53443265 6869 samtools_0.1.14-1.debian.tar.gz
- d7aa1cc47b6eeb4bac688ebb8ebd11108feda8f0d37471850a6d20609020d2c2 593618 samtools_0.1.14-1_amd64.deb
- 9722646d951eb7f65799b5838eeffadb170ed01e6348047e7ec97c403f68d09a 165312 libbam-dev_0.1.14-1_amd64.deb
+ dfabb3bac8229dfbd26e852cf9aebd90445512eee8891dfeec0bb56340ed9122 1939 samtools_0.1.15-1.dsc
+ 59cdd41c9697b5a2c8c57f1867266f8262058d280460d22cdd74606aa7d7047f 374429 samtools_0.1.15.orig.tar.bz2
+ f7f94edc5b59dd11e1dee11346cc11f25b15dae8869074d840b89535ea1a2b53 7005 samtools_0.1.15-1.debian.tar.gz
+ 5ab78897e9238eef643f4334cfc4cafd42531763fc97e619242cdbdcf5e42d3f 599104 samtools_0.1.15-1_amd64.deb
+ 303f88901a79909ed1b5bcefb3ccdd99b0c39e4a0f8fdf5b6d2010dff585a443 169002 libbam-dev_0.1.15-1_amd64.deb
Files:
- e17f770090ed9c540e9cf0e5a0100704 1939 science optional samtools_0.1.14-1.dsc
- aa2bed7b3d96e64cbeb3726f1fb6d880 370287 science optional samtools_0.1.14.orig.tar.bz2
- b3c31d72685018d26682d460667a77a8 6869 science optional samtools_0.1.14-1.debian.tar.gz
- d4018bd1b0f86e2caa76be65d162629c 593618 science optional samtools_0.1.14-1_amd64.deb
- 0c35b980860354f363a1011ea11bafe8 165312 libdevel optional libbam-dev_0.1.14-1_amd64.deb
+ 6b88fd8c962a8143d54b718dcfc5a01c 1939 science optional samtools_0.1.15-1.dsc
+ caf1cac191fdabd57a309e36f359c047 374429 science optional samtools_0.1.15.orig.tar.bz2
+ 8f3586257c58ea4371d4e83ebcb7a74e 7005 science optional samtools_0.1.15-1.debian.tar.gz
+ f11a7ccf86ab2a9b39be07d1191e3586 599104 science optional samtools_0.1.15-1_amd64.deb
+ 302c9810d2f9384ab504313a66e8beb8 169002 libdevel optional libbam-dev_0.1.15-1_amd64.deb
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diff --git a/amd64.log b/amd64.log
index 75047ee..39f2570 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,26 +1,26 @@
-sbuild (Debian sbuild) 0.62.1 (20 Mar 2011) on anx191
+sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on anx191
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (amd64) 29 Mar 2011 13:22 ║
+║ samtools 0.1.15-1 (amd64) 12 Apr 2011 19:54 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Distribution: unstable
Architecture: amd64
-I: NOTICE: Log filtering will replace '/build/samtools-1cRb9h' with 'BUILDDIR'
-I: NOTICE: Log filtering will replace '/var/lib/schroot/mount/sid-amd64-sbuild-3db42e15-0b96-4c9c-9601-7c786fbde54a' with 'CHROOT'
+I: NOTICE: Log filtering will replace 'build/samtools-uPEbZJ' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-874fd008-a454-4a94-ad87-a3cabe614343' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Hit http://ftp.jp.debian.org sid InRelease
-Get:1 http://ftp.jp.debian.org sid/main amd64 Packages/DiffIndex [2038 B]
-Hit http://ftp.jp.debian.org sid/main TranslationIndex
-Fetched 2038 B in 0s (3880 B/s)
+Hit http://ftp.riken.jp sid InRelease
+Hit http://ftp.riken.jp sid/main Sources/DiffIndex
+Hit http://ftp.riken.jp sid/main amd64 Packages/DiffIndex
+Hit http://ftp.riken.jp sid/main TranslationIndex
Reading package lists...
Reading package lists...
Building dependency tree...
@@ -35,14 +35,14 @@ Reading state information...
Local sources
─────────────
-samtools_0.1.14-1.dsc exists in .; copying to chroot
+samtools_0.1.15-1.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-3C_rcI/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-RyGduq/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -58,15 +58,15 @@ The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/706 B of archives.
+Need to get 0 B/702 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously deselected package sbuild-build-depends-core-dummy.
-(Reading database ... 10292 files and directories currently installed.)
+(Reading database ... 10291 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `BUILDDIR/resolver-CUSO_g/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-uzfR0a/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
Reading package lists...
@@ -95,17 +95,17 @@ The following NEW packages will be installed:
sbuild-build-depends-samtools-dummy zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/11.1 MB of archives.
+Need to get 0 B/11.2 MB of archives.
After this operation, 31.3 MB of additional disk space will be used.
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10292 files and directories currently installed.)
+(Reading database ... 10291 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_amd64.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-5_amd64.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_amd64.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_amd64.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.1-1_amd64.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_amd64.deb) ...
Selecting previously deselected package file.
@@ -119,7 +119,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_amd64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_amd64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ...
Selecting previously deselected package libunistring0.
@@ -127,15 +127,15 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_amd64.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_amd64.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_amd64.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_amd64.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_amd64.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_amd64.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_amd64.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_amd64.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
Selecting previously deselected package sbuild-build-depends-samtools-dummy.
@@ -145,7 +145,7 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
+Setting up man-db (2.6.0.1-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
@@ -153,16 +153,16 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.2-1) ...
+Setting up libglib2.0-0 (2.28.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
@@ -171,8 +171,8 @@ Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.21.0.20110327-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-7 gcc-4.5_4.5.2-7 libc6-dev_2.11.2-13 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-7 linux-libc-dev_2.6.38-1
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-2 cpp-4.5_4.5.2-7 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-2 g++-4.5_4.5.2-7 gcc_4:4.5.2-2 gcc-4.4-base_4.4.5-14 gcc-4.5_4.5.2-7 gcc-4.5-base_4.5.2-7 gcc-4.6-base_4.6.0-1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6_2.11.2-13 libc6-dev_2.11.2-13 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-1 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-7 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011d-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-3 dpkg-dev_1.16.0.1 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 libc6-dev_2.11.2-13 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 linux-libc-dev_2.6.38-3
+Package versions: apt_0.8.13.2 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-3 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-5 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-5 g++-4.5_4.5.2-8 gcc_4:4.5.2-5 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6_2.11.2-13 libc6-dev_2.11.2-13 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-3 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -182,10 +182,13 @@ Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binuti
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (samtools_0.1.14-1.dsc)
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Tue Apr 12 10:53:14 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -201,41 +204,41 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
+dpkg-buildpackage: source version 0.1.15-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build samtools-0.1.14
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture amd64
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 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `BUILDDIR/samtools-0.1.14'
-make[2]: Entering directory `BUILDDIR/samtools-0.1.14'
+make[1]: Entering directory `/«BUILDDIR»/samtools-0.1.15'
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `BUILDDIR/samtools-0.1.14'
-make[2]: Entering directory `BUILDDIR/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15'
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/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 `BUILDDIR/samtools-0.1.14/bcftools'
-make[2]: Entering directory `BUILDDIR/samtools-0.1.14/misc'
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `BUILDDIR/samtools-0.1.14/misc'
-make[1]: Leaving directory `BUILDDIR/samtools-0.1.14'
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/misc'
+make[1]: Leaving directory `/«BUILDDIR»/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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-0.1.14
+ dpkg-source -b samtools-0.1.15
dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: info: building samtools using existing ./samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: building samtools in samtools_0.1.14-1.debian.tar.gz
-dpkg-source: info: building samtools in samtools_0.1.14-1.dsc
+dpkg-source: info: building samtools using existing ./samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: building samtools in samtools_0.1.15-1.debian.tar.gz
+dpkg-source: info: building samtools in samtools_0.1.15-1.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/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `BUILDDIR/samtools-0.1.14'
-make[2]: Entering directory `BUILDDIR/samtools-0.1.14'
+make[1]: Entering directory `/«BUILDDIR»/samtools-0.1.15'
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -249,15 +252,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `BUILDDIR/samtools-0.1.14'
-make[2]: Entering directory `BUILDDIR/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/«BUILDDIR»/samtools-0.1.15'
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -268,10 +272,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `BUILDDIR/samtools-0.1.14/bcftools'
-make[2]: Entering directory `BUILDDIR/samtools-0.1.14/misc'
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `BUILDDIR/samtools-0.1.14/misc'
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -289,25 +293,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `BUILDDIR/samtools-0.1.14'
-make[3]: Entering directory `BUILDDIR/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15'
+make[3]: Entering directory `/«BUILDDIR»/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `BUILDDIR/samtools-0.1.14'
-make[3]: Entering directory `BUILDDIR/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/«BUILDDIR»/samtools-0.1.15'
+make[3]: Entering directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `BUILDDIR/samtools-0.1.14/bcftools'
-make[3]: Entering directory `BUILDDIR/samtools-0.1.14/misc'
+make[3]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/«BUILDDIR»/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `BUILDDIR/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `BUILDDIR/samtools-0.1.14'
-make[2]: Entering directory `BUILDDIR/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15'
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `BUILDDIR/samtools-0.1.14/bcftools'
-make[2]: Entering directory `BUILDDIR/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -317,14 +322,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `BUILDDIR/samtools-0.1.14/misc'
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `BUILDDIR/samtools-0.1.14'
+make[1]: Leaving directory `/«BUILDDIR»/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `BUILDDIR/samtools-0.1.14/examples'
+make[1]: Entering directory `/«BUILDDIR»/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -348,12 +353,12 @@ make[1]: Entering directory `BUILDDIR/samtools-0.1.14/examples'
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
+<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `BUILDDIR/samtools-0.1.14/examples'
+make[1]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary
test -x debian/rules
@@ -387,7 +392,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README BUILDDIR/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /«BUILDDIR»/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -412,7 +417,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' BUILDDIR/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /«BUILDDIR»/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -427,18 +432,18 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.15-1_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=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_amd64.deb'.
- dpkg-genchanges >../samtools_0.1.14-1_amd64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.15-1_amd64.deb'.
+ dpkg-genchanges >../samtools_0.1.15-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build samtools-0.1.14
+ dpkg-source --after-build samtools-0.1.15
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-1323
+Build finished at 20110412-1955
Finished
────────
@@ -450,15 +455,15 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_amd64.changes:
+samtools_0.1.15-1_amd64.changes:
────────────────────────────────
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: source amd64
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -467,45 +472,48 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- b4b787bd76c986989c7694bb6e9cdc7ffa64d6f2 1053 samtools_0.1.14-1.dsc
- 03d537ae69afa1607ba3f88a45aaff27d3ba4bd1 370287 samtools_0.1.14.orig.tar.bz2
- 3363682d767cc5aad089f40c49e3c70484da5be2 6869 samtools_0.1.14-1.debian.tar.gz
- cd07ae55e6c70a148ec68e60de7d32ae58adb733 593618 samtools_0.1.14-1_amd64.deb
- 1ad8d4c64330f90a6d3b60cd2a06dce44fa1ef41 165312 libbam-dev_0.1.14-1_amd64.deb
+ 20f6292bd8be9f1b76132e75ef3d5a2455001a8d 1053 samtools_0.1.15-1.dsc
+ 0a0f05928ba40ce95d4feda0cd0742ccd1b69e76 374429 samtools_0.1.15.orig.tar.bz2
+ bc8b3ec45fc1bd706858596b68661a654678b46e 7005 samtools_0.1.15-1.debian.tar.gz
+ 4f5a23bdbaa730c3c5e11e4e5792a00c9c0e5d3b 599104 samtools_0.1.15-1_amd64.deb
+ 473799f45bf22dde0d9d89b1a84a3529d1c85840 169002 libbam-dev_0.1.15-1_amd64.deb
Checksums-Sha256:
- 1b12c881d8b4a944ea81cd12a420e653c1f81ccd09763591c47ecc4798e461bb 1053 samtools_0.1.14-1.dsc
- 8bbe8fe4240fe98868891a27093e86ffb3149b716d9659db28c84df0c91d5975 370287 samtools_0.1.14.orig.tar.bz2
- 048f6988bbc21acd19f54e2f42ed105834981220f35a32397c6c202c53443265 6869 samtools_0.1.14-1.debian.tar.gz
- d7aa1cc47b6eeb4bac688ebb8ebd11108feda8f0d37471850a6d20609020d2c2 593618 samtools_0.1.14-1_amd64.deb
- 9722646d951eb7f65799b5838eeffadb170ed01e6348047e7ec97c403f68d09a 165312 libbam-dev_0.1.14-1_amd64.deb
+ d53980cf064401993dd0f0c63207d3b4d0a81780f9d0dd8d7d6fba1c9e850162 1053 samtools_0.1.15-1.dsc
+ 59cdd41c9697b5a2c8c57f1867266f8262058d280460d22cdd74606aa7d7047f 374429 samtools_0.1.15.orig.tar.bz2
+ f7f94edc5b59dd11e1dee11346cc11f25b15dae8869074d840b89535ea1a2b53 7005 samtools_0.1.15-1.debian.tar.gz
+ 5ab78897e9238eef643f4334cfc4cafd42531763fc97e619242cdbdcf5e42d3f 599104 samtools_0.1.15-1_amd64.deb
+ 303f88901a79909ed1b5bcefb3ccdd99b0c39e4a0f8fdf5b6d2010dff585a443 169002 libbam-dev_0.1.15-1_amd64.deb
Files:
- 5694dd95bd348ab7c85b1933b780c2ac 1053 science optional samtools_0.1.14-1.dsc
- aa2bed7b3d96e64cbeb3726f1fb6d880 370287 science optional samtools_0.1.14.orig.tar.bz2
- b3c31d72685018d26682d460667a77a8 6869 science optional samtools_0.1.14-1.debian.tar.gz
- d4018bd1b0f86e2caa76be65d162629c 593618 science optional samtools_0.1.14-1_amd64.deb
- 0c35b980860354f363a1011ea11bafe8 165312 libdevel optional libbam-dev_0.1.14-1_amd64.deb
+ fd5e8017924e6f29a496bcdf9a6612de 1053 science optional samtools_0.1.15-1.dsc
+ caf1cac191fdabd57a309e36f359c047 374429 science optional samtools_0.1.15.orig.tar.bz2
+ 8f3586257c58ea4371d4e83ebcb7a74e 7005 science optional samtools_0.1.15-1.debian.tar.gz
+ f11a7ccf86ab2a9b39be07d1191e3586 599104 science optional samtools_0.1.15-1_amd64.deb
+ 302c9810d2f9384ab504313a66e8beb8 169002 libdevel optional libbam-dev_0.1.15-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_amd64.deb
+samtools_0.1.15-1_amd64.deb
───────────────────────────
new debian package, version 2.0.
- size 593618 bytes: control archive= 1785 bytes.
+ size 599104 bytes: control archive= 1787 bytes.
786 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1072
+ Installed-Size: 1088
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -518,23 +526,23 @@ samtools_0.1.14-1_amd64.deb
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 2011-03-29 13:23 ./
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/lib/samtools/
--rwxr-xr-x root/root 11880 2011-03-29 13:23 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 19248 2011-03-29 13:23 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8560 2011-03-29 13:23 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 8128 2011-03-29 13:23 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 8224 2011-03-29 13:23 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/bin/
--rwxr-xr-x root/root 376080 2011-03-29 13:23 ./usr/bin/samtools
--rwxr-xr-x root/root 24768 2011-03-29 13:23 ./usr/bin/razip
--rwxr-xr-x root/root 106280 2011-03-29 13:23 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11880 2011-04-12 19:55 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 19248 2011-04-12 19:55 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8560 2011-04-12 19:55 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 8128 2011-04-12 19:55 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 8224 2011-04-12 19:55 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/bin/
+-rwxr-xr-x root/root 384272 2011-04-12 19:55 ./usr/bin/samtools
+-rwxr-xr-x root/root 24768 2011-04-12 19:55 ./usr/bin/razip
+-rwxr-xr-x root/root 114088 2011-04-12 19:55 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/samtools/
-rwxr-xr-x root/root 18572 2011-03-22 12:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2011-03-29 13:23 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-04-12 19:55 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 4996 2010-11-17 13:16 ./usr/share/samtools/interpolate_sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 13:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 13:16 ./usr/share/samtools/psl2sam.pl
@@ -546,43 +554,43 @@ drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/samtools/
-rwxr-xr-x root/root 2415 2010-11-17 13:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 13:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 5989 2010-11-17 13:16 ./usr/share/samtools/novo2sam.pl
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/man/man1/
--rw-r--r-- root/root 2005 2011-03-29 13:23 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 430 2011-03-29 13:23 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-03-29 13:23 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/doc/samtools/
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/doc/samtools/examples/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/man/man1/
+-rw-r--r-- root/root 2005 2011-04-12 19:55 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 430 2011-04-12 19:55 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-04-12 19:55 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 13:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 13:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 764 2010-11-17 13:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-03-29 13:23 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-04-12 19:55 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 886 2010-11-17 13:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 13:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 33578 2011-03-02 04:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 8225 2011-03-22 12:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 9003 2011-04-11 07:33 ./usr/share/doc/samtools/NEWS.gz
-rw-r--r-- root/root 916 2010-11-17 13:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 13:05 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1966 2011-03-29 13:23 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1296 2011-03-29 13:14 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 1031 2011-03-29 12:51 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2011-03-29 12:51 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 5287 2011-04-12 19:43 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1966 2011-04-12 19:55 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1362 2011-04-12 19:45 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1031 2011-04-12 19:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 592 2011-04-12 19:33 ./usr/share/doc/samtools/reference
-libbam-dev_0.1.14-1_amd64.deb
+libbam-dev_0.1.15-1_amd64.deb
─────────────────────────────
new debian package, version 2.0.
- size 165312 bytes: control archive= 900 bytes.
+ size 169002 bytes: control archive= 900 bytes.
674 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 460
+ Installed-Size: 472
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -593,23 +601,23 @@ libbam-dev_0.1.14-1_amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/lib/
--rw-r--r-- root/root 314106 2011-03-29 13:23 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/include/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/lib/
+-rw-r--r-- root/root 323908 2011-04-12 19:55 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/include/
-rw-r--r-- root/root 17815 2011-03-02 04:50 ./usr/include/khash.h
-rw-r--r-- root/root 3188 2010-11-17 13:16 ./usr/include/faidx.h
--rw-r--r-- root/root 4580 2011-03-22 12:09 ./usr/include/bgzf.h
--rw-r--r-- root/root 24165 2011-03-22 12:09 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 4617 2011-04-11 07:33 ./usr/include/bgzf.h
+-rw-r--r-- root/root 24338 2011-04-11 07:33 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 33578 2011-03-02 04:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 8225 2011-03-22 12:09 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 9003 2011-04-11 07:33 ./usr/share/doc/libbam-dev/NEWS.gz
-rw-r--r-- root/root 916 2010-11-17 13:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 13:05 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 1296 2011-03-29 13:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5287 2011-04-12 19:43 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1362 2011-04-12 19:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -621,7 +629,7 @@ drwxr-xr-x root/root 0 2011-03-29 13:23 ./usr/share/doc/libbam-dev/
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging CHROOTBUILDDIR
+Purging /«CHROOT»/«BUILDDIR»
Reading package lists...
Building dependency tree...
Reading state information...
@@ -637,7 +645,7 @@ The following packages will be REMOVED:
sbuild-build-depends-samtools-dummy* zlib1g-dev*
0 upgraded, 0 newly installed, 22 to remove and 0 not upgraded.
After this operation, 31.3 MB disk space will be freed.
-(Reading database ... 11735 files and directories currently installed.)
+(Reading database ... 11732 files and directories currently installed.)
Removing sbuild-build-depends-samtools-dummy ...
Removing cdbs ...
Removing debhelper ...
@@ -677,17 +685,17 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 12048
-Build-Time: 20
+Build-Space: 12208
+Build-Time: 21
Distribution: unstable
-Install-Time: 26
-Job: samtools_0.1.14-1.dsc
+Install-Time: 28
+Job: samtools_0.1.15-1.dsc
Package: samtools
-Package-Time: 48
-Source-Version: 0.1.14-1
-Space: 12048
+Package-Time: 51
+Source-Version: 0.1.15-1
+Space: 12208
Status: successful
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-1323
-Build needed 00:00:48, 12048k disc space
+Finished at 20110412-1955
+Build needed 00:00:51, 12208k disc space
diff --git a/dsc b/dsc
index 027dd03..0814b66 100644
--- a/dsc
+++ b/dsc
@@ -5,39 +5,39 @@ Format: 3.0 (quilt)
Source: samtools
Binary: samtools, libbam-dev
Architecture: any
-Version: 0.1.14-1
+Version: 0.1.15-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>
Dm-Upload-Allowed: yes
Homepage: http://samtools.sourceforge.net
-Standards-Version: 3.9.1
+Standards-Version: 3.9.2
Vcs-Browser: http://git.debian.org/?p=debian-med/samtools.git
Vcs-Git: git://git.debian.org/debian-med/samtools.git
Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checksums-Sha1:
- 03d537ae69afa1607ba3f88a45aaff27d3ba4bd1 370287 samtools_0.1.14.orig.tar.bz2
- 3363682d767cc5aad089f40c49e3c70484da5be2 6869 samtools_0.1.14-1.debian.tar.gz
+ 0a0f05928ba40ce95d4feda0cd0742ccd1b69e76 374429 samtools_0.1.15.orig.tar.bz2
+ bc8b3ec45fc1bd706858596b68661a654678b46e 7005 samtools_0.1.15-1.debian.tar.gz
Checksums-Sha256:
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- 048f6988bbc21acd19f54e2f42ed105834981220f35a32397c6c202c53443265 6869 samtools_0.1.14-1.debian.tar.gz
+ 59cdd41c9697b5a2c8c57f1867266f8262058d280460d22cdd74606aa7d7047f 374429 samtools_0.1.15.orig.tar.bz2
+ f7f94edc5b59dd11e1dee11346cc11f25b15dae8869074d840b89535ea1a2b53 7005 samtools_0.1.15-1.debian.tar.gz
Files:
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- b3c31d72685018d26682d460667a77a8 6869 samtools_0.1.14-1.debian.tar.gz
+ caf1cac191fdabd57a309e36f359c047 374429 samtools_0.1.15.orig.tar.bz2
+ 8f3586257c58ea4371d4e83ebcb7a74e 7005 samtools_0.1.15-1.debian.tar.gz
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--
Processing of sequence alignments in SAM and BAM formats.
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