Git log: commit 2b7a1c63b1ce8119f6ee576155af7efc39d872d1
Author: Steffen Moeller <moeller@debian.org>
Date: Sun Sep 10 11:33:20 2017 +0200
Added references to registries
commit 7f525ad6da62b79b1910f5b44c94a14c064a622a
Author: Andreas Tille <tille@debian.org>
Date: Fri Aug 4 18:55:59 2017 +0200
Do not warn about cwl-runner , upload to unstable
commit d3b6113420da7dad521d9ce5f53c9a9148b95148
Author: Andreas Tille <tille@debian.org>
Date: Fri Aug 4 17:56:47 2017 +0200
Add recommends to cwl-tool and fix shebang line of cwl scripts
commit 3c0ec5c15af181094f5aca31d65cc589cccd5bda
Author: Andreas Tille <tille@debian.org>
Date: Thu Jul 20 12:18:15 2017 +0200
Bump versioned Build-Depends: libhts-dev (>= 1.5)
commit d52cd132acd26dd53fd97ddd670c11e6be641268
Author: Andreas Tille <tille@debian.org>
Date: Thu Jul 20 12:17:05 2017 +0200
Standards-Version: 4.0.0 (no changes needed)
commit 3092088150ea98f786cd04516d64ceff67066f75
Author: Andreas Tille <tille@debian.org>
Date: Thu Jul 20 12:16:28 2017 +0200
debhelper 10
commit 1655d1e2edbade14fa8e81efbdcef96bf66ecaed
Author: Andreas Tille <tille@debian.org>
Date: Thu Jul 20 12:15:04 2017 +0200
New upstream version
commit 5eef358408da5e86c3365139744723915ee67d9b
Merge: ae32134 8a06c51
Author: Andreas Tille <tille@debian.org>
Date: Thu Jul 20 12:14:22 2017 +0200
Updated version 1.5 from '1.5'
with Debian dir 1f9b98601b18347e19cc5281a1b3b962281ce872
commit 8a06c510e8e5a19fc0b4115e252b654029642434
Author: Andreas Tille <tille@debian.org>
Date: Thu Jul 20 12:14:20 2017 +0200
New upstream version 1.5
commit ae32134425b32940de620ffae81084bf57c1c719
Author: Andreas Tille <tille@debian.org>
Date: Sun Jun 18 21:12:00 2017 +0200
Close bug, upload to unstable
commit dd7a11720720b1a1c5ecb5e0598115dec9dce596
Author: Andreas Tille <tille@debian.org>
Date: Sun Jun 18 21:07:39 2017 +0200
New upstream version
commit 2ba4095f05d88f8b1cb30977dd75d5109df28122
Merge: 32563cc 8f8600a
Author: Andreas Tille <tille@debian.org>
Date: Sun Jun 18 21:04:10 2017 +0200
Merge tag '1.4.1' into debian/unstable
Release 1.4.1 (8th May 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Added options to fastq to create fastq files from BC (or other)
tags.
* Samtools view has gained a -G <flags> option to exclude on all bits
set. For example to discard reads where neither end has been
mapped use "-G 12".
* Samtools cat has a -b <fofn> option to ease concatenation of many
files.
* Added misc/samtools_tab_completion for bash auto-completion of
samtools sub-commands. (#560)
* Samtools tview now has J and K keys for verticale movement by 20
lines. (#257)
* Various compilation / portability improvements.
* Fixed issue with more than 65536 CIGAR operations and SAM/CRAM files.
(#667)
commit 32563cce4ae4e8efbe4270f60d6340c83cf835ce
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 21:43:13 2017 +0100
Rebuild against properly named libhts which had a soname change
commit 7e76eb3f5cd98a34b0ad86faccdd1fb78c3ee008
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 19:16:55 2017 +0100
Bump versioned Depends: libhts-dev (>= 1.4), upload to experimental
commit 0dafb696ee61a6fb2a1b9c6bcbceab68283ba307
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 16:29:23 2017 +0100
Adapt patches
commit f83cd5e8518b5a0f838502e2d37e07fc5bdc2e50
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 16:26:52 2017 +0100
Replaced Dominique Belhachemi by my own ID as Uploader
commit bda1d8abf284c755a16c68e8feb9541ebab5f153
Merge: 0bc88ca 0a859b1
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 16:23:40 2017 +0100
Merge tag '1.4' into debian/unstable
Release 1.4 (13 March 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Noteworthy changes in samtools:
* Fixed Issue #345 - out-by-one error in insert-size in samtools stats
* bam_split now add a @PG header to the bam file
* Added mate cigar tag support to fixmate
* Multi-threading is now supported for decoding BAM and CRAM (as well
as the previously supported encoding). Most commands that read BAM
or CRAM have gained an -@ or --threads arguments, providing a
significant speed bonus. For commands that both read and write
files the threads are shared between decoding and encoding tasks.
* Added -a option to samtools mpileup to show all locations, including
sites with zero depth; repeating the option as -aa or -a -a additionally
shows reference sequences without any reads mapped to them (#496).
* The mpileup text output no longer contains empty columns at zero coverage
positions. Previously it would output "...0\t\t..." in some circumstances
(zero coverage due to being below a minumum base quality); this has been
fixed to output as "...0\t*\t*..." with placeholder '*' characters as in
other zero coverage circumstances (see PR #537).
* To stop it from creating too many temporary files, samtools sort
will now not run unless its per-thread memory limit (-m) is set to
at least 1 megabyte (#547).
* The misc/plot-bamstats script now has a -l / --log-y option to change
various graphs to display their Y axis log-scaled. Currently this
affects the Insert Size graph (PR #589; thanks to Anton Kratz).
* Fixmate will now also add and update MC (mate CIGAR) tags.
commit 0bc88cabb43b1cc43b61acbe7fd0d37531a8dfe6
Author: Andreas Tille <tille@debian.org>
Date: Sun Jan 15 10:02:15 2017 +0100
Remove wrong debian-changes patch
commit 861db4215321ed8649dc0f33ebdeb48a989689c4
Author: Andreas Tille <tille@debian.org>
Date: Sun Jan 15 10:00:32 2017 +0100
Please use UNRELEASED as long as a package is not uploaded
commit 11b2ae7173e729dd1a78106482bcea7efadf6706
Author: Anton Khodak <anton.khodak@ukr.net>
Date: Sat Jan 14 09:01:44 2017 -0800
minor fixes
commit 129288348521ba3ad532d4ba24eb3a5ccb74b703
Author: Anton Khodak <anton.khodak@ukr.net>
Date: Thu Jan 12 00:33:24 2017 -0800
Add CWL tools
commit 2b8f06d7375aa40d45f2634ff008389b4be1acf9
Author: Anton Khodak <anton.khodak@ukr.net>
Date: Thu Jan 12 00:30:46 2017 -0800
Add CWL tools to the package
commit 4dae08be7c8d166e9c8ff48d4c30fd26ecc1c71d
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Mon Oct 24 16:33:37 2016 +0200
dch -r
commit 070aa3e4ec96606da81ea2050f351d40cc9de3db
Author: Sascha Steinbiss <satta@debian.org>
Date: Sun Oct 23 13:36:03 2016 +0000
adjust d/changelog
commit 90a26350479e956eb45e6ff98c4e5d034f16929c
Author: Sascha Steinbiss <satta@debian.org>
Date: Sun Oct 23 13:33:06 2016 +0000
fall back to working ax_with_curses.m4
commit db8bac6a829060fb990e30fd8b19c28d40500939
Author: Sascha Steinbiss <satta@debian.org>
Date: Sun Oct 23 13:31:23 2016 +0000
use John Marshall's patch to address test pty issue
commit 9aac9cbec983831351611d227702fc04b7235948
Author: Sascha Steinbiss <satta@debian.org>
Date: Thu Oct 20 20:03:25 2016 +0000
fix FTBFS
commit a98b89bbd5e258c91e86100ad275aa1d031590f8
Author: Charles Plessy <plessy@debian.org>
Date: Sun May 8 21:11:34 2016 +0900
samtools (1.3.1-2) unstable; urgency=medium
952da10 Build-depends on htslib 1.3.1. (Closes: #822701)
-- Charles Plessy <plessy@debian.org> Sun, 08 May 2016 21:11:12 +0900
commit 0296398891f288d2f2be78654d3b699f2bceb8f4
Author: Charles Plessy <plessy@debian.org>
Date: Wed Apr 27 10:03:06 2016 +0900
Current changelog.
commit 952da102acfa75de77f1b5902b10aa3f065f181d
Author: Charles Plessy <plessy@debian.org>
Date: Wed Apr 27 10:02:02 2016 +0900
Needs htslib 1.3.1.
Closes: #822701
commit 60c45b7e8943124488c9cdbc231e32d8c95316c8
Author: Charles Plessy <plessy@debian.org>
Date: Tue Apr 26 21:12:25 2016 +0900
samtools (1.3.1-1) unstable; urgency=medium
0c961b2 Merge tag '1.3.1' into debian/unstable
3666b08 Conforms with Policy version 3.9.8.
-- Charles Plessy <plessy@debian.org> Tue, 26 Apr 2016 21:12:05 +0900
commit 82c3bfa5864096b40617beaca72d125fff7710a7
Author: Charles Plessy <plessy@debian.org>
Date: Tue Apr 26 20:58:18 2016 +0900
Remove legacy statement on the libbam.
commit 3666b08edb66c6bd1597552348b883370e8a2cb2
Author: Charles Plessy <plessy@debian.org>
Date: Tue Apr 26 20:57:11 2016 +0900
Conforms with Policy version 3.9.8.
commit 0de58f79d6c25a3fd7869bd0870163a2e424b088
Author: Charles Plessy <plessy@debian.org>
Date: Tue Apr 26 20:42:02 2016 +0900
New upstream release; no new copyright nor license notice.
commit 0c961b23afec6697b7dbe7cc91e246f694b9ac1e
Merge: 096bc41 897c002
Author: Charles Plessy <plessy@debian.org>
Date: Tue Apr 26 20:39:39 2016 +0900
Merge tag '1.3.1' into debian/unstable
Samtools release 1.3.1: bug fixes, notably sort temporary files
* The sort command creates any needed temporary files alongside the final
output file (similarly to the pre-1.3 behaviour), and now aborts when
it detects a collision with another sort invocation's temporary files.
When the -T PREFIX option specified is a directory (or when sorting to
standard output), a random component is now added to temporary filenames
to try to avoid collisions (#432, #523, #529, #535, PR #530).
* All samtools commands now check for I/O errors more carefully, especially
when writing output files (#111, #253, #470, PR #467).
* Build fixes for 32-bit systems; be sure to run configure on such systems
to enable large file support and access to 2GiB+ files.
* The fasta/fastq/bam2fq command no longer ignores reads when the -s option
is used (#532).
* The fastq -O option no longer crashes on reads that do not have an OQ tag
field (#517).
* The merge and sort commands now handle (unusual) BAM files that have no
textual @SQ headers (#548, #550).
* Sorting files containing @CO headers no longer duplicates the comment
headers, which previously happened on large sorts for which temporary
files were needed (#563).
* The rmdup and view -l commands no longer crash on @RG headers that do not
have a LB field (#538).
* Fixed miscellaneous issues #128, #130, #131, #489, and #514.
commit 096bc41752fe26844633cde88a7614cfde51c280
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Fri Feb 5 08:32:52 2016 +0000
dch -r
commit a9bf06a38a1061418cd19b0f63e855b43b661c36
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Fri Feb 5 08:29:26 2016 +0000
add NEWS for 1.3 commandline API changes
commit 9d12a17a18b199d4cf9245195112906e323d877b
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Wed Feb 3 09:35:39 2016 +0000
update d/changelog
commit 82f34d3480d43b8fe8d895c23ccffeeebc865e52
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sat Jan 30 21:38:54 2016 +0000
patch spelling
commit d985799b2098bde92d27bae258612856b3c41a41
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sat Jan 30 21:15:23 2016 +0000
add patch header
commit 487e759e70a8dfc77c7d23b1aa085d2a6f9d75ef
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sat Jan 30 20:49:56 2016 +0000
cleanup copyright
commit 6479cce74c8a54356d3cb72293378cb465799b36
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sat Jan 30 20:49:43 2016 +0000
add Build-Dep to automake
commit f1e3f7c8ee30f890f8bd8fbb07278b8e99a93666
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sat Jan 30 20:49:31 2016 +0000
patch configure.in to not call make in m4_esyscmd_s()
commit 45397bc4edcd2da0e80e18fc3e75c54800302847
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sat Jan 30 20:48:50 2016 +0000
use secure Vcs-Git
commit 4988ce7af84ee295f63c93f3185aeea407071ade
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sat Jan 30 15:44:43 2016 +0000
adapt to new build system
commit 5c4ca0b5309fa25e1ecd6790ad6eec269a75789f
Author: Charles Plessy <plessy@debian.org>
Date: Thu Dec 24 14:09:58 2015 +0900
Removed patch; issue solved upstream.
https://github.com/samtools/samtools/issues/305
commit c12f4f35b82b40a6b3d44236a89c543bac210bd9
Author: Charles Plessy <plessy@debian.org>
Date: Thu Dec 24 14:07:10 2015 +0900
Removed patch; issue solved upstream.
https://github.com/samtools/samtools/pull/286
commit 86a93751b87ad21154b8068d06e15d84f080edeb
Author: Charles Plessy <plessy@debian.org>
Date: Thu Dec 24 14:02:04 2015 +0900
Replace LDLIBS by LIBS, following upstream changelog.
commit 824f68f0227076c1e4573d894f3ee89a54632618
Author: Charles Plessy <plessy@debian.org>
Date: Thu Dec 24 13:59:30 2015 +0900
New upstream release; no new copyright nor license notice.
commit 95c561dc652f4d762d562504f52935270d585ab2
Merge: 4a5274b ed3191b
Author: Charles Plessy <plessy@debian.org>
Date: Thu Dec 24 13:55:19 2015 +0900
Merge tag '1.3' into debian/unstable
Samtools release 1.3: many improvements, fixes, new commands
* The obsolete "samtools sort in.bam out.prefix" usage has been removed.
If you are still using -f, -o, or out.prefix, convert to use -T PREFIX
and/or -o FILE instead. (#295, #349, #356, #418, PR #441; see also
discussions in #171, #213.)
* The "bamshuf" command has been renamed to "collate" (hence the term
bamshuf no longer appears in the documentation, though it still works
on the command line for compatibility with existing scripts).
* The mpileup command now outputs the unseen allele in VCF/BCF as <*>
rather than X or <X> as previously, and now has AD, ADF, ADR, INFO/AD,
INFO/ADF, INFO/ADR --output-tags annotations that largely supersede
the existing DV, DP4, DPR annotations.
* The mpileup command now applies BAQ calculations at all base positions,
regardless of which -l or -r options are used (previously with -l it was
not applied to the first few tens of bases of each chromosome, leading
to different mpileup results with -l vs. -r; #79, #125, #286, #407).
* Samtools now has a configure script which checks your build environment
and facilitates choosing which HTSlib to build against. See INSTALL
for details.
* Samtools's Makefile now fully supports the standard convention of
allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden as needed.
Previously it listened to $(LDLIBS) instead; if you were overriding
that, you should now override LIBS rather than LDLIBS.
* A new addreplacerg command that adds or alters @RG headers and RG:Z
record tags has been added.
* The rmdup command no longer immediately aborts (previously it always
aborted with "bam_get_library() not yet implemented"), but remains
not recommended for most use (#159, #252, #291, #393).
* Merging files with millions of headers now completes in a reasonable
amount of time (#337, #373, #419, #453; thanks to Nathan Weeks,
Chris Smowton, Martin Pollard, Rob Davies).
* Samtools index's optional index output path argument works again (#199).
* Fixed calmd, targetcut, and potential mpileup segfaults when given broken
alignments with POS far beyond the end of their reference sequences.
* If you have source code using bam_md.c's bam_fillmd1_core(), bam_cap_mapQ(),
or bam_prob_realn_core() functions, note that these now take an additional
ref_len parameter. (The versions named without "_core" are unchanged.)
* The tview command's colour scheme has been altered to be more suitable
for users with colour blindness (#457).
* Samtools depad command now handles CIGAR N operators and accepts
CRAM files (#201, #404).
* Samtools stats now outputs separate "N" and "other" columns in the
ACGT content per cycle section (#376).
* Added -a option to samtools depth to show all locations, including
zero depth sites (#374).
* New samtools dict command, which creates a sequence dictionary
(as used by Picard) from a FASTA reference file.
* Samtools stats --target-regions option works again.
* Added legacy API sam.h functions sam_index_load() and samfetch() providing
bam_fetch()-style iteration over either BAM or CRAM files. (In general
we recommend recoding against the htslib API directly, but this addition
may help existing libbam-using programs to be CRAM-enabled easily.)
* Fixed legacy API's samopen() to write headers only with "wh" when writing
SAM files. Plain "w" suppresses headers for SAM file output, but this
was broken in 1.2.
* "samtools fixmate - -" works in pipelines again; with 1.0 to 1.2,
this failed with "[bam_mating] cannot determine output format".
* Restored previous "samtools calmd -u" behaviour of writing compression
level 0 BAM files. Samtools 1.0 to 1.2 incorrectly wrote raw non-BGZF
BAM files, which cannot be read by most other tools. (Samtools commands
other than calmd were unaffected by this bug.)
* Restored bam_nt16_nt4_table[] to legacy API header bam.h.
* Fixed bugs #269, #305, #320, #328, #346, #353, #365, #392, #410, #445,
#462, #475, and #495.
commit 4a5274b48c80c97f05bb2f78215ad1a5d7c4083c
Merge: c740a12 663b1a8
Author: Charles Plessy <plessy@debian.org>
Date: Thu Dec 24 13:50:30 2015 +0900
Merge branch 'debian/unstable' of git+ssh://git.debian.org/git/debian-med/samtools into debian/unstable
commit 663b1a8ea3a586962d3fb99454ea5584411a2a3b
Author: Andreas Tille <tille@debian.org>
Date: Mon Dec 21 13:49:12 2015 +0100
Upload to unstable
commit 95188c1fce13f04f507f4ef60c2b6dc8f9355edd
Author: Andreas Tille <tille@debian.org>
Date: Mon Dec 21 13:48:54 2015 +0100
Provide some more manpages
commit 0777f64201bd5b2f3ec128a771351f840bebd9aa
Author: Andreas Tille <tille@debian.org>
Date: Mon Dec 21 13:24:01 2015 +0100
Fix Mayhem issues caused by unlimited reads of gz input
commit 9f6248cb89494a43e3d3bcfeeb93d56b5bb66ecc
Author: Andreas Tille <tille@debian.org>
Date: Tue Sep 22 16:24:22 2015 +0200
Mark as team upload since I do not intend to become Uploader for samtools
commit 8a507bc2aa4d250e48d901315dd9ab64d794011f
Author: Andreas Tille <tille@debian.org>
Date: Tue Sep 22 16:23:33 2015 +0200
Fix spelling
commit 477fe9904a0796483bb9d5f0de6f89b3f25d1f1b
Author: Andreas Tille <tille@debian.org>
Date: Tue Sep 22 16:22:47 2015 +0200
Add lintian-override to document that the language extensions are used internally
commit 32bbc4518877052c5ec19abb93fbdb3b2ec79aa0
Author: Andreas Tille <tille@debian.org>
Date: Tue Sep 22 16:17:26 2015 +0200
Fix synopsis and vcs-browser
commit 0662664019ce89ac0e09315767b22a688f5ff96e
Author: Afif Elghraoui <afif@ghraoui.name>
Date: Tue Sep 22 06:54:59 2015 -0700
Prepare for upload
commit 658179c6e1ac91d3f71882f7653f72d3f93c95b9
Author: Afif Elghraoui <afif@ghraoui.name>
Date: Tue Sep 22 06:41:10 2015 -0700
Revert "Remove source files not present in upstream tarball"
This reverts commit 702d28926f97b3acb9ce92705cbbe28b41015615.
This does not really cause a major problem.
commit 19de55eeac5cc4f635720eb857f427ba091237d7
Author: Afif Elghraoui <afif@ghraoui.name>
Date: Tue Sep 22 06:39:58 2015 -0700
Revert "Allow all scripts to be called without language extensions"
This reverts commit 7afd302dc02a8c4521017b68a3db4063ff86c4ac.
Closes: #799698
commit 6691fed22acb37d156000f4c6b699a03ccbfd714
Author: Charles Plessy <plessy@debian.org>
Date: Thu Sep 17 20:23:10 2015 +0900
samtools (1.2-2) unstable; urgency=medium
[ Afif Elghraoui ]
eb56918 Add patch to fix building on i386
702d289 Remove source files not present in upstream tarball
7afd302 Allow all scripts to be called without language extensions
[ Charles Plessy ]
876f680 Document the update workflow of the source package's repository.
-- Charles Plessy <plessy@debian.org> Thu, 17 Sep 2015 20:21:15 +0900
commit 876f680fec0be152a7175764ed4920ce0dcc8307
Author: Charles Plessy <plessy@debian.org>
Date: Thu Sep 17 20:18:41 2015 +0900
Note that this source package is managed like htslib.
This message should point to the Debian Med Policy once it is updated.
commit c740a12b1a8f3fde3f4878f1c1067c40e05f7c24
Author: Charles Plessy <plessy@debian.org>
Date: Wed Sep 16 18:02:31 2015 +0900
Revert "Remove source files not present in upstream tarball"
This reverts commit 702d28926f97b3acb9ce92705cbbe28b41015615.
commit c76e08da944a26ffd7867bf0a47ff40802d6f0bf
Author: Afif Elghraoui <afif@ghraoui.name>
Date: Sun Sep 13 22:29:26 2015 -0700
Mark release and remove redundant changelog entry
commit c6cefd5c59c2f1ea3e69bd83570adb103a11ea35
Author: Afif Elghraoui <afif@ghraoui.name>
Date: Sun Sep 13 22:20:24 2015 -0700
Update changelog for 1.2-2 release
commit 7afd302dc02a8c4521017b68a3db4063ff86c4ac
Author: Afif Elghraoui <afif@ghraoui.name>
Date: Sun Sep 13 22:19:17 2015 -0700
Allow all scripts to be called without language extensions
commit 702d28926f97b3acb9ce92705cbbe28b41015615
Author: Afif Elghraoui <afif@ghraoui.name>
Date: Sun Sep 13 21:08:18 2015 -0700
Remove source files not present in upstream tarball
I'm not sure how they got there, but they cause problems
when building the package.
commit eb56918001cda9174a4d7078d91d171e158772d7
Author: Afif Elghraoui <afif@ghraoui.name>
Date: Sun Sep 13 18:51:50 2015 -0700
Add patch to fix building on i386
commit 2f148b1560fdf1f6df1cb6fd467e9f81670a7df1
Author: Afif Elghraoui <afif@ghraoui.name>
Date: Sun Sep 13 18:49:19 2015 -0700
Set up a new changelog entry
commit e4c31091a774ee5b44f5b1d5f6c5e6b180a09796
Author: Charles Plessy <plessy@debian.org>
Date: Tue Jun 16 06:58:56 2015 +0900
samtools (1.2-1) unstable; urgency=medium
a5f28a0 Merge tag '1.2' into debian/unstable
c542e84 Build-depend on libhts-dev 1.2.
6c2d9cd Build-depend and recommend libio-pty-perl.
(Needed for the regression tests.)
23e44a4 Removed fix_coverage_cap.patch, obsoleted by -d option.
1091aab Refreshed fuzzy patches.
-- Charles Plessy <plessy@debian.org> Tue, 16 Jun 2015 06:12:12 +0900
commit affb220a30e7a4a3f31b43ecc801bcdca4b31d85
Author: Charles Plessy <plessy@debian.org>
Date: Tue Jun 16 05:30:38 2015 +0900
Current changelog.
commit d2e84d56065aaee4842360f2e067ff5e3af8a2b0
Author: Charles Plessy <plessy@debian.org>
Date: Tue Jun 16 05:30:09 2015 +0900
Revert last commit, that included patched files by mistake.
This reverts commit c789e05419a795fa01a162aa84419f856d5385b8.
commit c789e05419a795fa01a162aa84419f856d5385b8
Author: Charles Plessy <plessy@debian.org>
Date: Mon Jun 15 22:03:26 2015 +0900
Current changelog.
commit c542e84fd612419a7cf0f3caa1439c0870334d62
Author: Charles Plessy <plessy@debian.org>
Date: Mon Jun 15 21:59:57 2015 +0900
Build-depend on libhts-dev 1.2.
commit 1091aab090d557e3891bf99e3d1271ffd852dc4c
Author: Charles Plessy <plessy@debian.org>
Date: Mon Jun 15 21:46:58 2015 +0900
Refreshed fuzzy patches.
commit 23e44a4110a57524a37a013e8eedf3bbc37c9541
Author: Charles Plessy <plessy@debian.org>
Date: Mon Jun 15 21:44:28 2015 +0900
Removed fix_coverage_cap.patch, obsoleted by -d option.
See https://github.com/samtools/samtools/issues/284
commit 712a2160145fbced8404adb8f54218f99da731e5
Author: Charles Plessy <plessy@debian.org>
Date: Mon Jun 15 21:43:54 2015 +0900
Corrected syntax.
commit 71af052b8ae35cb9ad1e1962c70b1d222e6e7937
Author: Charles Plessy <plessy@debian.org>
Date: Mon Jun 15 21:31:44 2015 +0900
New upstream release ; no new copyright notice nor license term.
commit a5f28a0f7a32c48ea7241913cec87fce0de35ab3
Merge: 6ce5671 255f97d
Author: Charles Plessy <plessy@debian.org>
Date: Mon Jun 15 21:23:53 2015 +0900
Merge tag '1.2' into debian/unstable
Bug fix release
commit 6ce5671a6ef57e75490e4c3d6dbded71c6612ad3
Author: Charles Plessy <plessy@debian.org>
Date: Wed Oct 1 17:52:37 2014 +0900
Make autopkg test depend on tabix.
commit d3946de853e86ecd11a7a15dab9445d364c65d37
Author: Charles Plessy <plessy@debian.org>
Date: Thu Sep 25 21:40:28 2014 +0900
Current changelog.
commit 6c2d9cd543036264833eca4d3e1a3483d78cc914
Author: Charles Plessy <plessy@debian.org>
Date: Thu Sep 25 20:54:09 2014 +0900
Build-depend and recommend libio-pty-perl for the regression tests.
commit 91356d65b732a7d22a7fff994f9c6d17d75568e3
Author: Charles Plessy <plessy@debian.org>
Date: Thu Sep 25 09:05:17 2014 +0900
samtools (1.1-1) unstable; urgency=medium
c448d48 Merge tag '1.1' into debian/unstable
d12ab1e Merge branch 'develop' into debian/unstable to solve issue
with regression tests needing a pseudo-terminal.
See https://github.com/samtools/samtools/issues/300
c87f8ce Add autopkg tests.
7c50b7b Removed python-wrong-path-for-interpreter.patch
(issue solved upstream).
-- Charles Plessy <plessy@debian.org> Thu, 25 Sep 2014 09:04:20 +0900
commit dcc1da7a658c5739aee7144e5e92c6b93db09cdc
Author: Charles Plessy <plessy@debian.org>
Date: Thu Sep 25 08:55:37 2014 +0900
Removed sed command redundant with patch dynamic-build.patch.
commit 7c50b7b7bf5a47a81b0a8c355c634600bcfe7291
Author: Charles Plessy <plessy@debian.org>
Date: Thu Sep 25 08:54:27 2014 +0900
Removed python-wrong-path-for-interpreter.patch, solved upstream.
commit d12ab1ed118c324825bf3bae9996bbe59862f9d7
Merge: c448d48 b7c4b4d
Author: Charles Plessy <plessy@debian.org>
Date: Thu Sep 25 08:22:21 2014 +0900
Merge branch 'develop' into debian/unstable
commit c448d4848f865dbebe33bd6cd520f66fb5745986
Merge: 1f661b2 68ca977
Author: Charles Plessy <plessy@debian.org>
Date: Thu Sep 25 08:22:09 2014 +0900
Merge tag '1.1' into debian/unstable
Bug fix release
commit 1f661b25822072560bde42a3b591d2931c5cdd61
Author: Charles Plessy <plessy@debian.org>
Date: Tue Sep 23 18:32:48 2014 +0900
Current changelog.
commit c87f8ce95e97ca11d98309812bc02c2c0c988190
Author: Charles Plessy <plessy@debian.org>
Date: Tue Sep 23 18:31:59 2014 +0900
Add autopkg tests.
commit 8c928df20f8190d3ce139a074e23536987b285df
Author: Charles Plessy <plessy@debian.org>
Date: Tue Sep 23 10:07:01 2014 +0900
samtools (1.0-1) unstable; urgency=low
[ Charles Plessy ]
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.
0446ed7 Conforms with Policy 3.5.6.
* 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.
edc09e4 Prevent Makefile from including local copy of the HTSlib.
* 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.
[ Andreas Tille ]
f69f412 Versioned Build-Depends libhts-dev >= 1.0
-- Charles Plessy <plessy@debian.org> Tue, 23 Sep 2014 09:36:27 +0900
commit 0446ed7cae33c2f4faec8969df26f6f702841ff2
Author: Charles Plessy <plessy@debian.org>
Date: Tue Sep 23 08:32:11 2014 +0900
Conforms with Policy 3.5.6.
commit f69f412352db56f3f0ac519df3906862f49a5607
Author: Andreas Tille <tille@debian.org>
Date: Mon Sep 22 12:26:29 2014 +0200
Versioned Build-Depends libhts-dev >= 1.0
commit 6b2c8c94f8e25f2e727457c2dfc1785e1d2cfb6b
Author: Charles Plessy <plessy@debian.org>
Date: Thu Sep 18 07:34:47 2014 +0900
Current changelog.
commit 8a118f663a209ff48f9cc6fa6067c064b019e123
Author: Charles Plessy <plessy@debian.org>
Date: Wed Sep 17 08:12:12 2014 +0900
Build-depend on libhts-dev...
commit 932819f028041d11f70270ec5648f6161095722b
Author: Charles Plessy <plessy@debian.org>
Date: Wed Sep 17 06:58:07 2014 +0900
Build for Unstable.
commit edc09e477372b7791e7f00734d325f3e8d04c398
Author: Charles Plessy <plessy@debian.org>
Date: Wed Sep 17 06:54:22 2014 +0900
Prevent Makefile from including local copy of the HTSlib.
commit 3d6431d16cb7f21e6c318cc9cecdb0cebe0fa14a
Merge: 66e256b 9be3811
Author: Charles Plessy <plessy@debian.org>
Date: Wed Sep 17 06:47:20 2014 +0900
Merge branch 'debian/experimental' into debian/unstable
commit 9be38118d45c2819cc672043f9b9be8ed771a9bd
Author: Charles Plessy <plessy@debian.org>
Date: Sat Aug 23 16:19:45 2014 +0900
samtools (1.0-1~experimental) experimental; urgency=low
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.
-- Charles Plessy <plessy@debian.org> Sat, 23 Aug 2014 16:02:12 +0900
commit 5e834656ad3689f64dca661af265d143cb0851a8
Author: Charles Plessy <plessy@debian.org>
Date: Sat Aug 23 16:01:35 2014 +0900
Branch to build packages for Experimental.
