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git.donarmstrong.com Git - samtools.git/log
Petr Danecek [Fri, 11 Jun 2010 15:58:20 +0000 (15:58 +0000)]
Initial release on behalf of Aylwyn Scally
Petr Danecek [Fri, 7 May 2010 12:41:56 +0000 (12:41 +0000)]
Added a note about the indels coordinates
Petr Danecek [Fri, 23 Apr 2010 13:42:13 +0000 (13:42 +0000)]
Added the possibility to print or not to print the reference allele
Petr Danecek [Thu, 15 Apr 2010 08:33:55 +0000 (08:33 +0000)]
More descriptive message for space separated tags
Petr Danecek [Wed, 14 Apr 2010 15:44:50 +0000 (15:44 +0000)]
Speedup with -i, no need to query the reference all the time
Petr Danecek [Mon, 15 Mar 2010 14:03:51 +0000 (14:03 +0000)]
Fixed the order of sequences in the header
Petr Danecek [Thu, 4 Mar 2010 11:28:35 +0000 (11:28 +0000)]
Added possibility to select indels only and fixed a bug in reporting homozygous indels.
On behalf of John Marshall [Sat, 27 Feb 2010 11:48:17 +0000 (11:48 +0000)]
Improve the invalid 'BAM\1' magic number error message, and also print it
when no bytes can be read from the alleged BAM file, e.g., in the common
user error case when a SAM file has accidentally been supplied.
Petr Danecek [Fri, 26 Feb 2010 15:51:40 +0000 (15:51 +0000)]
Improved efficiency of header parsing
Heng Li [Wed, 24 Feb 2010 02:08:48 +0000 (02:08 +0000)]
Updated export2sam.pl by Chris Saunders from Illumina.
Petr Danecek [Wed, 17 Feb 2010 13:32:53 +0000 (13:32 +0000)]
Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
Petr Danecek [Fri, 12 Feb 2010 09:52:37 +0000 (09:52 +0000)]
Print an error for pileups in simple format
Heng Li [Thu, 11 Feb 2010 19:01:41 +0000 (19:01 +0000)]
added a hidden option in pileup to output the base position (for Erin)
Petr Danecek [Tue, 9 Feb 2010 15:12:14 +0000 (15:12 +0000)]
Added possibility to specify a custom column title for the data column
Petr Danecek [Tue, 9 Feb 2010 14:46:09 +0000 (14:46 +0000)]
Added the -d option to limit maximum depth for indels.
Petr Danecek [Wed, 3 Feb 2010 12:57:27 +0000 (12:57 +0000)]
Added VCF header
Heng Li [Mon, 1 Feb 2010 14:13:19 +0000 (14:13 +0000)]
* samtools-0.1.7-6
* fixed a bug in faidx
On behalf of John Marshall [Mon, 11 Jan 2010 23:51:49 +0000 (23:51 +0000)]
Put the right filename in the error message.
Heng Li [Mon, 14 Dec 2009 16:26:47 +0000 (16:26 +0000)]
* samtools-0.1.7-5 (r528)
* further add new consensus generation strategy
Petr Danecek [Fri, 11 Dec 2009 17:31:05 +0000 (17:31 +0000)]
Fixed a bug in knet_seek
Petr Danecek [Fri, 11 Dec 2009 12:51:18 +0000 (12:51 +0000)]
Small fix in VCF format: dot for the empty INFO field
Petr Danecek [Fri, 11 Dec 2009 09:36:18 +0000 (09:36 +0000)]
Allow tabs in the CO header field
On behalf of John Marshall [Thu, 10 Dec 2009 15:03:58 +0000 (15:03 +0000)]
Depend on libbam.a rather than the phony target, so that samtools is not
unnecessarily rebuilt every time. Also clean bgzip.
On behalf of John Marshall [Thu, 10 Dec 2009 14:45:32 +0000 (14:45 +0000)]
Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
is defined. Also introduce $(KNETFILE_O) which can be set to empty to
facilitate non-knet builds.
Heng Li [Tue, 1 Dec 2009 18:02:36 +0000 (18:02 +0000)]
* samtools-0.1.7-4 (r522)
* fixed a bug in "view -r"
* added a new option "view -R" to read required read groups from a file
Heng Li [Tue, 1 Dec 2009 15:00:12 +0000 (15:00 +0000)]
* samtools-0.1.7-3 (r521)
* calmd: optionally mask matching bases as N
Heng Li [Tue, 1 Dec 2009 14:37:17 +0000 (14:37 +0000)]
* samtools-0.1.7-2 (r520)
* fixed a few issues with compilation in Windows (on behalf of John)
* choose a random base as the consensus (for population genetics studies)
On behalf of John Marshall [Mon, 30 Nov 2009 15:53:02 +0000 (15:53 +0000)]
Put libraries at the end, so they can resolve references from libbam.a
as well, even with old-fashioned linkers.
Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
the freshly built library, not some other libbam.a lying around the system.
On behalf of John Marshall [Mon, 30 Nov 2009 13:44:56 +0000 (13:44 +0000)]
Also clean *.exe (for Cygwin users using this makefile).
On behalf of John Marshall [Mon, 30 Nov 2009 12:09:04 +0000 (12:09 +0000)]
Index files should be opened in binary mode, not text mode.
Heng Li [Fri, 27 Nov 2009 20:18:59 +0000 (20:18 +0000)]
another example program
Heng Li [Fri, 27 Nov 2009 15:44:56 +0000 (15:44 +0000)]
* samtools-0.1.7-1 (r515)
* report an error when .fai contains duplicated names, instead of segfault
On behalf of John Marshall [Tue, 24 Nov 2009 14:45:35 +0000 (14:45 +0000)]
Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
Heng Li [Mon, 16 Nov 2009 15:13:07 +0000 (15:13 +0000)]
Update Makefile.mingw for the same reason
Heng Li [Mon, 16 Nov 2009 15:00:08 +0000 (15:00 +0000)]
Fixed a bug in compiling razip
Heng Li [Tue, 10 Nov 2009 15:55:41 +0000 (15:55 +0000)]
Release samtools-0.1.7 (r510)
Heng Li [Fri, 6 Nov 2009 14:17:09 +0000 (14:17 +0000)]
* samtools-0.1.6-22 (r509)
* forget to fix a similar problem in glfgen
Heng Li [Fri, 6 Nov 2009 14:06:40 +0000 (14:06 +0000)]
* samtools-0.1.6-21 (r508)
* fixed a potential bug in the indel caller towards the end of a chromosome
Heng Li [Mon, 26 Oct 2009 15:38:00 +0000 (15:38 +0000)]
* samtools-0.1.6-19 (r494)
* allow to convert Illumina quality (64 based) to the BAM quality
Heng Li [Mon, 26 Oct 2009 14:24:39 +0000 (14:24 +0000)]
* samtools-0.1.6-18 (r493)
* fixed the bugs due to improperly incorporating Petr's header parser
* a little code clean up in sam_header.c
Petr Danecek [Sat, 24 Oct 2009 13:43:25 +0000 (13:43 +0000)]
Added sam_header_line_free call for sam_header_parse2
Heng Li [Sat, 24 Oct 2009 04:50:16 +0000 (04:50 +0000)]
* BUGGY VERSION
* fixed a minor bug
Heng Li [Sat, 24 Oct 2009 04:45:12 +0000 (04:45 +0000)]
* BUGGY VERSION
* improved the interface a bit
* bug unfixed
Heng Li [Sat, 24 Oct 2009 04:41:50 +0000 (04:41 +0000)]
* BUGGY VERSION. Please NOT use it.
* Fixed a minor bug, but the major bug is still there.
Heng Li [Sat, 24 Oct 2009 04:17:10 +0000 (04:17 +0000)]
* This revision is SERIOUSLY BUGGY. Please NOT use it.
* Start to incorporate header parsing from Petr Danecek
Petr Danecek [Fri, 23 Oct 2009 15:44:32 +0000 (15:44 +0000)]
Now possible to merge multiple HeaderDict dictionaries
Petr Danecek [Thu, 22 Oct 2009 15:46:58 +0000 (15:46 +0000)]
Petr Danecek [Thu, 22 Oct 2009 15:41:56 +0000 (15:41 +0000)]
Heng Li [Mon, 19 Oct 2009 18:31:32 +0000 (18:31 +0000)]
* samtools-0.1.6-17 (r484)
* fixed a memory leak in rmdupse
* fixed a bug in parsing @RG header lines
* test rmdup in examples/
Heng Li [Mon, 19 Oct 2009 17:22:48 +0000 (17:22 +0000)]
* samtools-0.1.6-16 (r483)
* unify the interface of rmdup and rmdupse
* a new bug found in rg2lib(). Have not been fixed yet.
Heng Li [Mon, 19 Oct 2009 17:03:34 +0000 (17:03 +0000)]
* samtools-0.1.6-15 (r482)
* rewrite rmdupse
* rmdupse is now library aware
Heng Li [Sun, 18 Oct 2009 04:07:21 +0000 (04:07 +0000)]
* samtools-0.1.6-14 (r480)
* rmdup is now RG aware
Heng Li [Sun, 18 Oct 2009 02:05:20 +0000 (02:05 +0000)]
added a small unitity to parse SRA XML files
Heng Li [Sun, 18 Oct 2009 00:57:26 +0000 (00:57 +0000)]
* samtools-0.1.6-13 (r479)
* merge: optionally use file names as RG tags
Heng Li [Wed, 14 Oct 2009 18:18:12 +0000 (18:18 +0000)]
* samtools-0.1.6-12 (r478)
* fixed a bug in the indel caller
Heng Li [Sat, 10 Oct 2009 10:12:26 +0000 (10:12 +0000)]
* samtools-0.1.6-11 (r477)
* fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
Petr Danecek [Fri, 9 Oct 2009 15:45:36 +0000 (15:45 +0000)]
Added the sam2vcf.pl script.
Heng Li [Thu, 8 Oct 2009 14:19:16 +0000 (14:19 +0000)]
Unfinished modification. Please do not use this revision...
Petr Danecek [Thu, 8 Oct 2009 10:39:54 +0000 (10:39 +0000)]
Removed the offending knet_seek message.
Petr Danecek [Tue, 6 Oct 2009 13:26:35 +0000 (13:26 +0000)]
Bug fix - faidx on RAZF compressed files now working.
Heng Li [Fri, 2 Oct 2009 12:42:57 +0000 (12:42 +0000)]
Clarify the meaning of a region like "chr2:1,000,000".
Heng Li [Fri, 2 Oct 2009 09:42:19 +0000 (09:42 +0000)]
Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
Heng Li [Tue, 29 Sep 2009 19:01:27 +0000 (19:01 +0000)]
* samtools-0.1.6-9 (r470)
* make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
Heng Li [Tue, 29 Sep 2009 12:07:44 +0000 (12:07 +0000)]
* samtools-0.1.6-9 (r469)
* refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
Heng Li [Mon, 28 Sep 2009 09:18:29 +0000 (09:18 +0000)]
* samtools-0.1.6-7 (r468)
* make merge stable
Petr Danecek [Mon, 28 Sep 2009 08:51:29 +0000 (08:51 +0000)]
Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
Heng Li [Thu, 24 Sep 2009 10:29:19 +0000 (10:29 +0000)]
* samtools-0.1.6-6 (r466)
* do not crash calmd when some sequences are absent from the reference.
On behalf of John Marshall [Wed, 23 Sep 2009 10:14:32 +0000 (10:14 +0000)]
Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
no way to seek on a pipe and the messages always appear.
Petr Danecek [Wed, 16 Sep 2009 11:05:41 +0000 (11:05 +0000)]
A bug fix, "samtools view" is now working again.
Heng Li [Wed, 16 Sep 2009 08:51:07 +0000 (08:51 +0000)]
* samtools-0.1.6-5 (r462)
* Added knetfile support in razf and faidx (on behalf of Petr Danecek)
Heng Li [Wed, 9 Sep 2009 11:06:22 +0000 (11:06 +0000)]
fixed a formatting issue
Heng Li [Tue, 8 Sep 2009 22:14:08 +0000 (22:14 +0000)]
* samtools-0.1.6-4 (r459)
* make sort output the result to stdout when -o is in use
Heng Li [Mon, 7 Sep 2009 09:10:28 +0000 (09:10 +0000)]
* samtools-0.1.6-2 (r458)
* added more interface to faidx (by Nils)
* updated documentation
Heng Li [Sat, 5 Sep 2009 20:12:04 +0000 (20:12 +0000)]
* samtools-0.1.6-2 (r457)
* get rid of three assert() in bam_sort.c
On behalf of John Marshall [Fri, 4 Sep 2009 16:46:25 +0000 (16:46 +0000)]
Return NULL from _razf_open() (and hence razf_open()/razf_open2())
when opening the file fails.
Heng Li [Wed, 2 Sep 2009 12:56:33 +0000 (12:56 +0000)]
Release samtools-0.1.6
Heng Li [Wed, 2 Sep 2009 09:44:48 +0000 (09:44 +0000)]
* samtools-0.1.5-34 (r451)
* applied the patch by John
* improved the help message a little bit
Heng Li [Wed, 2 Sep 2009 08:55:55 +0000 (08:55 +0000)]
* samtools-0.1.5-33 (r450)
* fixed a bug in bam_color.c (on behalf of Nils Homer)
Heng Li [Sat, 29 Aug 2009 19:36:41 +0000 (19:36 +0000)]
* samtools-0.1.5-32 (r449)
* fillmd: fixed a bug in modifying MD/NM tags
* in import, give a warning if the read is aligned but there is no CIGAR.
Heng Li [Wed, 19 Aug 2009 08:44:28 +0000 (08:44 +0000)]
* samtools-0.1.5-31 (r448)
* fixed an issue when the last CIGAR is I or D
Heng Li [Mon, 17 Aug 2009 08:34:57 +0000 (08:34 +0000)]
* samtools-0.1.5-30 (r447)
* fixed a bug in bam_aux_get(): 'A' is not checked
Heng Li [Mon, 17 Aug 2009 08:33:17 +0000 (08:33 +0000)]
*
Heng Li [Tue, 11 Aug 2009 09:02:36 +0000 (09:02 +0000)]
* samtools-0.1.5-28 (r444)
* bug in "merge -n"
Heng Li [Tue, 11 Aug 2009 08:29:11 +0000 (08:29 +0000)]
* samtools-0.1.5-27 (r443)
* SEQ and QUAL can be "*"
* parse CIGAR "=" and "X" as "M"
Heng Li [Fri, 7 Aug 2009 20:56:38 +0000 (20:56 +0000)]
* samtools-0.1.5-26 (r442)
* replace RSA Inc md5.* with ones under permissive lincense
* fixed a bug in detecting unsorted bam in pileup
On behalf of Bob Handsaker [Wed, 5 Aug 2009 13:41:28 +0000 (13:41 +0000)]
Change copyright notices now that MIT has approved open source distribution.
Heng Li [Wed, 5 Aug 2009 09:44:24 +0000 (09:44 +0000)]
* samtools-0.1.5-25 (r436)
* in flagstats, do not report singletons if both ends are unmapped
Heng Li [Tue, 4 Aug 2009 21:16:51 +0000 (21:16 +0000)]
fixed a SERIOUS bug in setting 0x20 flag
Heng Li [Tue, 4 Aug 2009 20:50:43 +0000 (20:50 +0000)]
fixed two minor bugs (suggested by Tim M Storm)
Heng Li [Tue, 4 Aug 2009 08:13:24 +0000 (08:13 +0000)]
* samtools-0.1.5-24 (r435)
* fixed a typo
Heng Li [Mon, 3 Aug 2009 09:40:42 +0000 (09:40 +0000)]
* samtools-0.1.5-23 (r434)
* in tview, press 'r' to show read names rather than sequences
Heng Li [Sun, 2 Aug 2009 18:13:35 +0000 (18:13 +0000)]
* tried to fixed the buggy FTP random access in Windows. FAILED.
* anyway, MinGW seems to have problem with "%lld".
Heng Li [Sat, 1 Aug 2009 23:32:07 +0000 (23:32 +0000)]
* samtools-0.1.5-22 (r432)
* faidx: fixed compitability issue with _WIN32
* razf: fixed potential compitability issue with _WIN32
* PDCurses support in Windows
Heng Li [Sat, 1 Aug 2009 22:34:54 +0000 (22:34 +0000)]
replace the GnuWin32 version of libz.a with my own build with MinGW.
Heng Li [Sat, 1 Aug 2009 22:21:07 +0000 (22:21 +0000)]
add comments
Heng Li [Sat, 1 Aug 2009 21:41:19 +0000 (21:41 +0000)]
* samtools-0.1.5-21 (r428)
* knetfile.c is now compatible with mingw-winsock
Heng Li [Fri, 31 Jul 2009 23:39:07 +0000 (23:39 +0000)]
simplify MinGW Makefile
Heng Li [Fri, 31 Jul 2009 23:30:54 +0000 (23:30 +0000)]
* samtools-0.1.5-20 (r427)
* MinGW support. At least SAM<->BAM conversion is working. Other
functionality are not tested at the moment.
* zlib headers and Windows version of libz.a are included in win32/
Heng Li [Fri, 31 Jul 2009 22:32:09 +0000 (22:32 +0000)]
* samtools-0.1.5-19 (r426)
* fixed a bug caused by recent modifications. Sorry.
Heng Li [Fri, 31 Jul 2009 22:23:51 +0000 (22:23 +0000)]
compatible with Windows binary files