samtools.git
9 years agorazf.c: replaced many calloc() calls with one large calloc() using RAZF_STRUCT_SIZE... hamrhein
Henry Amrhein [Tue, 15 Jan 2013 22:54:50 +0000 (14:54 -0800)]
razf.c:  replaced many calloc() calls with one large calloc() using RAZF_STRUCT_SIZE macro

9 years agorazf.h: added RAZF_STRUCT_SIZE macro
Henry Amrhein [Tue, 15 Jan 2013 22:54:24 +0000 (14:54 -0800)]
razf.h:  added RAZF_STRUCT_SIZE macro

9 years agorazf.c:
Henry Amrhein [Thu, 3 Jan 2013 22:49:36 +0000 (14:49 -0800)]
razf.c:
realloc() wrapper didn't assign the new pointer upon success.

9 years agorazf.c:
Henry Amrhein [Thu, 3 Jan 2013 18:54:57 +0000 (10:54 -0800)]
razf.c:
wrapped all calls to malloc(), calloc(), and realloc() with
error-checking.

9 years agorazf.c
Henry Amrhein [Thu, 3 Jan 2013 06:53:51 +0000 (22:53 -0800)]
razf.c
wrapped calls to read() and write() with error-checking

started wrapping malloc() and calloc() calls with error-checking

9 years agoknetfile.c
Henry Amrhein [Thu, 3 Jan 2013 06:37:30 +0000 (22:37 -0800)]
knetfile.c
wrapped netwrite() calls with error-checking

9 years agobam_index.c:
Henry Amrhein [Thu, 3 Jan 2013 06:16:32 +0000 (22:16 -0800)]
bam_index.c:
added error checking for malloc(), calloc() and realloc() calls.

9 years agobam_cat.c:
Henry Amrhein [Wed, 2 Jan 2013 20:58:36 +0000 (12:58 -0800)]
bam_cat.c:
check return value of malloc() in bam_cat()

wrapped fwrite() calls with error-checking

9 years agobam_index.c:
Henry Amrhein [Wed, 2 Jan 2013 20:35:14 +0000 (12:35 -0800)]
bam_index.c:
wrapped fread() and fwrite() calls with error checking

removed unused and duplicated endian-swap after writing
n-chunks for big-endian systems in bam_index_save()

10 years agoMention ‘SAMtools’ in libbam-dev's description, to make it easier to find with apt... master remotes/origin/lucid
Charles Plessy [Thu, 15 Sep 2011 04:29:42 +0000 (13:29 +0900)]
Mention ‘SAMtools’ in libbam-dev's description, to make it easier to find with apt-cache.

10 years agoStarting the work on next package update.
Charles Plessy [Thu, 15 Sep 2011 04:27:01 +0000 (13:27 +0900)]
Starting the work on next package update.

10 years agoUploading 0.1.18-1 to unstable.
Charles Plessy [Tue, 6 Sep 2011 08:30:24 +0000 (17:30 +0900)]
Uploading 0.1.18-1 to unstable.

10 years agoAdded a DEP 3 header to debian/patches/no-pileup-tests.patch.
Charles Plessy [Tue, 6 Sep 2011 07:48:32 +0000 (16:48 +0900)]
Added a DEP 3 header to debian/patches/no-pileup-tests.patch.

10 years agoCompress binary packages with xz.
Charles Plessy [Tue, 6 Sep 2011 07:36:06 +0000 (16:36 +0900)]
Compress binary packages with xz.

10 years agoNew upstream release.
Charles Plessy [Tue, 6 Sep 2011 06:55:14 +0000 (15:55 +0900)]
New upstream release.

Updated copyright statements.

10 years agoMerge commit 'upstream/0.1.18'
Charles Plessy [Tue, 6 Sep 2011 06:48:40 +0000 (15:48 +0900)]
Merge commit 'upstream/0.1.18'

10 years agoImported Upstream version 0.1.18
Charles Plessy [Tue, 6 Sep 2011 06:48:39 +0000 (15:48 +0900)]
Imported Upstream version 0.1.18

10 years agoUploading samtools_0.1.17-1_amd64.changes.
Charles Plessy [Mon, 11 Jul 2011 12:11:11 +0000 (21:11 +0900)]
Uploading samtools_0.1.17-1_amd64.changes.

10 years agoPatched the example makefile to not use samtools pileup, deprecated.
Charles Plessy [Mon, 11 Jul 2011 12:02:37 +0000 (21:02 +0900)]
Patched the example makefile to not use samtools pileup, deprecated.

10 years agobcftools.1 and samtools.1 were merged in upstream release 0.1.17.
Charles Plessy [Mon, 11 Jul 2011 11:32:09 +0000 (20:32 +0900)]
bcftools.1 and samtools.1 were merged in upstream release 0.1.17.

10 years agoNew upstream release (no new copyright holder nor license statement).
Charles Plessy [Mon, 11 Jul 2011 11:26:09 +0000 (20:26 +0900)]
New upstream release (no new copyright holder nor license statement).

10 years agoMerge commit 'upstream/0.1.17'
Charles Plessy [Mon, 11 Jul 2011 11:18:59 +0000 (20:18 +0900)]
Merge commit 'upstream/0.1.17'

10 years agoImported Upstream version 0.1.17
Charles Plessy [Mon, 11 Jul 2011 11:18:58 +0000 (20:18 +0900)]
Imported Upstream version 0.1.17

11 years agoUploaded samtools_0.1.16-1_amd64.changes.
Charles Plessy [Thu, 19 May 2011 04:28:19 +0000 (13:28 +0900)]
Uploaded samtools_0.1.16-1_amd64.changes.

11 years agoMove the headers to /usr/include/samtools.
Charles Plessy [Thu, 19 May 2011 04:18:48 +0000 (13:18 +0900)]
Move the headers to /usr/include/samtools.

11 years agoDistribute transiently sam.h in /usr/include.
Charles Plessy [Sat, 7 May 2011 09:34:45 +0000 (18:34 +0900)]
Distribute transiently sam.h in /usr/include.

11 years agoAdded a configuration file to make it obvious git-buildpackage is used.
Charles Plessy [Sat, 7 May 2011 09:28:56 +0000 (18:28 +0900)]
Added a configuration file to make it obvious git-buildpackage is used.

11 years agoNew upstream release, introducing two files with new copyright statements.
Charles Plessy [Sat, 7 May 2011 08:59:18 +0000 (17:59 +0900)]
New upstream release, introducing two files with new copyright statements.

11 years agoMerge commit 'upstream/0.1.16'
Charles Plessy [Sat, 7 May 2011 08:30:17 +0000 (17:30 +0900)]
Merge commit 'upstream/0.1.16'

11 years agoImported Upstream version 0.1.16
Charles Plessy [Sat, 7 May 2011 08:30:16 +0000 (17:30 +0900)]
Imported Upstream version 0.1.16

11 years agoUploaded 0.1.15-1 to Sid.
Charles Plessy [Tue, 12 Apr 2011 10:46:31 +0000 (19:46 +0900)]
Uploaded 0.1.15-1 to Sid.

11 years agoNew upstream release (no new copyright notices).
Charles Plessy [Tue, 12 Apr 2011 10:44:14 +0000 (19:44 +0900)]
New upstream release (no new copyright notices).

11 years agoImported Upstream version 0.1.15
Charles Plessy [Tue, 12 Apr 2011 10:40:07 +0000 (19:40 +0900)]
Imported Upstream version 0.1.15

11 years agoMerge commit 'upstream/0.1.15'
Charles Plessy [Tue, 12 Apr 2011 10:40:07 +0000 (19:40 +0900)]
Merge commit 'upstream/0.1.15'

11 years ago # Uploaded samtools version 0.1.14-1.
Charles Plessy [Tue, 29 Mar 2011 04:34:44 +0000 (13:34 +0900)]
 # Uploaded samtools version 0.1.14-1.

11 years ago # New upstream release (new copyright notices and licenses proofchecked).
Charles Plessy [Tue, 29 Mar 2011 04:08:26 +0000 (13:08 +0900)]
 # New upstream release (new copyright notices and licenses proofchecked).

11 years agoImported Upstream version 0.1.14
Charles Plessy [Tue, 29 Mar 2011 03:52:27 +0000 (12:52 +0900)]
Imported Upstream version 0.1.14

11 years agoMerge commit 'upstream/0.1.14'
Charles Plessy [Tue, 29 Mar 2011 03:52:27 +0000 (12:52 +0900)]
Merge commit 'upstream/0.1.14'

11 years ago # Uploaded 0.1.13 to Sid.
Charles Plessy [Wed, 2 Mar 2011 05:10:04 +0000 (14:10 +0900)]
 # Uploaded 0.1.13 to Sid.

11 years ago # bcftools/bcf-fix.pl removed upstream.
Charles Plessy [Wed, 2 Mar 2011 05:09:53 +0000 (14:09 +0900)]
 # bcftools/bcf-fix.pl removed upstream.

11 years ago # Copyright review of the diff between 0.1.12 and 0.1.13.
Charles Plessy [Wed, 2 Mar 2011 04:38:09 +0000 (13:38 +0900)]
 # Copyright review of the diff between 0.1.12 and 0.1.13.

11 years agoImported Upstream version 0.1.13
Charles Plessy [Wed, 2 Mar 2011 04:30:55 +0000 (13:30 +0900)]
Imported Upstream version 0.1.13

11 years agoMerge commit 'upstream/0.1.13'
Charles Plessy [Wed, 2 Mar 2011 04:30:55 +0000 (13:30 +0900)]
Merge commit 'upstream/0.1.13'

11 years ago # Install the manual page of bcftools.
Charles Plessy [Wed, 2 Mar 2011 00:45:17 +0000 (09:45 +0900)]
 # Install the manual page of bcftools.

Closes: http://bugs.debian.org/616025
11 years ago# Uploaded 0.1.12a-1 to Debian.
Charles Plessy [Fri, 3 Dec 2010 05:07:52 +0000 (14:07 +0900)]
# Uploaded 0.1.12a-1 to Debian.

11 years ago# Use bzip2 compression for the binary packages and raised DH compat level.
Charles Plessy [Fri, 3 Dec 2010 04:31:13 +0000 (13:31 +0900)]
# Use bzip2 compression for the binary packages and raised DH compat level.

Reason: I am affraid that ‘--’ is not available in lower versions of debhelper.

11 years ago# New usptream release; no change for licenses or copyrights.
Charles Plessy [Fri, 3 Dec 2010 04:28:22 +0000 (13:28 +0900)]
# New usptream release; no change for licenses or copyrights.

11 years agoMerge commit 'upstream/0.1.12a'
Charles Plessy [Fri, 3 Dec 2010 04:24:40 +0000 (13:24 +0900)]
Merge commit 'upstream/0.1.12a'

11 years agoImported Upstream version 0.1.12a
Charles Plessy [Fri, 3 Dec 2010 04:24:39 +0000 (13:24 +0900)]
Imported Upstream version 0.1.12a

11 years agoMerge commit 'upstream/0.1.11'
Charles Plessy [Fri, 3 Dec 2010 04:24:35 +0000 (13:24 +0900)]
Merge commit 'upstream/0.1.11'

11 years agoImported Upstream version 0.1.11
Charles Plessy [Fri, 3 Dec 2010 04:24:34 +0000 (13:24 +0900)]
Imported Upstream version 0.1.11

11 years ago # New upstream release.
Charles Plessy [Wed, 17 Nov 2010 11:33:05 +0000 (20:33 +0900)]
 # New upstream release.

11 years agoMerge commit 'upstream/0.1.10'
Charles Plessy [Wed, 17 Nov 2010 11:23:17 +0000 (20:23 +0900)]
Merge commit 'upstream/0.1.10'

11 years agoImported Upstream version 0.1.10
Charles Plessy [Wed, 17 Nov 2010 11:23:16 +0000 (20:23 +0900)]
Imported Upstream version 0.1.10

11 years ago # New upstream release, and new program: bcftools.
Charles Plessy [Mon, 1 Nov 2010 11:06:52 +0000 (20:06 +0900)]
 # New upstream release, and new program: bcftools.

11 years ago # Install bcftools, its manpage, bcf-fix.pl, vcfutils.pl, and new examples.
Charles Plessy [Mon, 1 Nov 2010 11:05:07 +0000 (20:05 +0900)]
 # Install bcftools, its manpage, bcf-fix.pl, vcfutils.pl, and new examples.

11 years ago # Incremented Standards-Version to reflect conformance with Policy 3.9.1.
Charles Plessy [Mon, 1 Nov 2010 11:04:40 +0000 (20:04 +0900)]
 # Incremented Standards-Version to reflect conformance with Policy 3.9.1.

11 years ago # Updated and reformatted debian/copyright according to latest DEP-5 draft.
Charles Plessy [Mon, 1 Nov 2010 11:04:01 +0000 (20:04 +0900)]
 # Updated and reformatted debian/copyright according to latest DEP-5 draft.

11 years ago # New files in the new upstream release.
Charles Plessy [Mon, 1 Nov 2010 09:51:59 +0000 (18:51 +0900)]
 # New files in the new upstream release.

11 years agoImported Upstream version 0.1.9
Charles Plessy [Mon, 1 Nov 2010 09:45:04 +0000 (18:45 +0900)]
Imported Upstream version 0.1.9

11 years agoMerge commit 'upstream/0.1.9'
Charles Plessy [Mon, 1 Nov 2010 09:45:04 +0000 (18:45 +0900)]
Merge commit 'upstream/0.1.9'

11 years agoAdded notes on how the package is tested.
Charles Plessy [Wed, 14 Jul 2010 23:40:11 +0000 (08:40 +0900)]
Added notes on how the package is tested.

11 years agoNew upstream release, with among many changes a new python script.
Charles Plessy [Wed, 14 Jul 2010 05:19:47 +0000 (14:19 +0900)]
New upstream release, with among many changes a new python script.

11 years agoCopied from SVN revision 4710 and adapted to Git.
Charles Plessy [Wed, 14 Jul 2010 05:04:08 +0000 (14:04 +0900)]
Copied from SVN revision 4710 and adapted to Git.

11 years agoThis source package is managed with Git since upstream version 1.7~dfsg.
Charles Plessy [Tue, 13 Jul 2010 12:17:59 +0000 (21:17 +0900)]
This source package is managed with Git since upstream version 1.7~dfsg.

11 years agoCopyright notice bureaucracy.
Charles Plessy [Tue, 13 Jul 2010 12:12:20 +0000 (21:12 +0900)]
Copyright notice bureaucracy.

Addded a new paragraph to comply with Debian's requirement to document
all copyright statements.

11 years agoThe 1.8 tarball does not contain Windows binaries anymore.
Charles Plessy [Tue, 13 Jul 2010 12:08:27 +0000 (21:08 +0900)]
The 1.8 tarball does not contain Windows binaries anymore.

11 years agoMerge commit 'upstream/0.1.8'
Charles Plessy [Tue, 13 Jul 2010 12:02:50 +0000 (21:02 +0900)]
Merge commit 'upstream/0.1.8'

11 years agoImported Upstream version 0.1.8
Charles Plessy [Tue, 13 Jul 2010 12:02:49 +0000 (21:02 +0900)]
Imported Upstream version 0.1.8

11 years agoIn version 1.8, there are no binary files to remove from the upstream tarball.
Charles Plessy [Tue, 13 Jul 2010 11:56:30 +0000 (20:56 +0900)]
In version 1.8, there are no binary files to remove from the upstream tarball.

12 years agoUploaded package after misc. improvements.
Charles Plessy [Wed, 18 Nov 2009 05:31:10 +0000 (14:31 +0900)]
Uploaded package after misc. improvements.

  - Updated debian/copyright.
  - Polished and install new razip manual page.
  - Better clean the example directory to make the source package
    buildable twice in a row.

12 years agoTidied the minimalistic razip.1 manual page.
Charles Plessy [Tue, 17 Nov 2009 04:29:18 +0000 (13:29 +0900)]
Tidied the minimalistic razip.1 manual page.

12 years agoSimple manpage created with help2man.
Charles Plessy [Tue, 17 Nov 2009 04:07:53 +0000 (13:07 +0900)]
Simple manpage created with help2man.

  help2man --no-info --name "Compress and decompress files in RAZip format" ./razip > debian/razip.1

12 years agoMinor upstream update correcting a build failure.
Charles Plessy [Tue, 17 Nov 2009 01:34:56 +0000 (10:34 +0900)]
Minor upstream update correcting a build failure.

12 years agoMerge commit 'upstream/0.1.7a.dfsg'
Charles Plessy [Tue, 17 Nov 2009 01:33:36 +0000 (10:33 +0900)]
Merge commit 'upstream/0.1.7a.dfsg'

12 years agoImported Upstream version 0.1.7a~dfsg
Charles Plessy [Tue, 17 Nov 2009 01:33:35 +0000 (10:33 +0900)]
Imported Upstream version 0.1.7a~dfsg

12 years agoConverted to the source format ‘3.0 (quilt)’.
Charles Plessy [Mon, 16 Nov 2009 05:35:55 +0000 (14:35 +0900)]
Converted to the source format ‘3.0 (quilt)’.

12 years agoUpdate in preparation for new upstream release.
Charles Plessy [Mon, 16 Nov 2009 05:33:18 +0000 (14:33 +0900)]
Update in preparation for new upstream release.

12 years agoImported Upstream version 0.1.7~dfsg
Charles Plessy [Mon, 16 Nov 2009 05:23:42 +0000 (14:23 +0900)]
Imported Upstream version 0.1.7~dfsg

12 years agoMerge commit 'upstream/0.1.7.dfsg'
Charles Plessy [Mon, 16 Nov 2009 05:23:42 +0000 (14:23 +0900)]
Merge commit 'upstream/0.1.7.dfsg'

12 years agoImported Debian patch 0.1.6~dfsg-1
Charles Plessy [Mon, 14 Sep 2009 12:58:36 +0000 (21:58 +0900)]
Imported Debian patch 0.1.6~dfsg-1

12 years agoImported Upstream version 0.1.6~dfsg
Charles Plessy [Mon, 14 Sep 2009 13:27:26 +0000 (22:27 +0900)]
Imported Upstream version 0.1.6~dfsg

12 years agoMerge branch 'upstream'
Charles Plessy [Mon, 14 Sep 2009 13:27:26 +0000 (22:27 +0900)]
Merge branch 'upstream'

12 years agoImported Debian patch 0.1.5c-2
Charles Plessy [Thu, 3 Sep 2009 10:29:40 +0000 (19:29 +0900)]
Imported Debian patch 0.1.5c-2

12 years agoImported Debian patch 0.1.5c-1
Charles Plessy [Sun, 16 Aug 2009 05:38:20 +0000 (14:38 +0900)]
Imported Debian patch 0.1.5c-1

12 years agoImported Upstream version 0.1.5c
Charles Plessy [Tue, 8 Sep 2009 10:38:06 +0000 (19:38 +0900)]
Imported Upstream version 0.1.5c