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git.donarmstrong.com Git - samtools.git/log
Heng Li [Fri, 23 Jul 2010 17:25:44 +0000 (17:25 +0000)]
added an alternative prior
Heng Li [Fri, 23 Jul 2010 15:48:51 +0000 (15:48 +0000)]
calculate posterior allele frequency
Heng Li [Fri, 23 Jul 2010 01:39:13 +0000 (01:39 +0000)]
* samtools-0.1.8-3 (r627)
* multi-sample snp calling appears to work. More tests needed.
Heng Li [Thu, 22 Jul 2010 20:37:56 +0000 (20:37 +0000)]
* preliminary multisample SNP caller.
* something looks not so right, but it largely works
Heng Li [Wed, 14 Jul 2010 20:26:27 +0000 (20:26 +0000)]
* samtools-0.1.8-2 (r617)
* allele frequency calculation apparently works...
Heng Li [Wed, 14 Jul 2010 17:33:51 +0000 (17:33 +0000)]
* added mutli-sample framework. It is not working, yet.
* improved the mpileup interface
Heng Li [Tue, 13 Jul 2010 18:50:12 +0000 (18:50 +0000)]
* samtools-0.1.8-1 (r615)
* allow to get mpileup at required sites
Heng Li [Mon, 12 Jul 2010 02:40:56 +0000 (02:40 +0000)]
Release samtools-0.1.8
Heng Li [Mon, 12 Jul 2010 01:08:56 +0000 (01:08 +0000)]
fixed a compiling issue for Windows
Heng Li [Mon, 12 Jul 2010 00:59:15 +0000 (00:59 +0000)]
fixed a bug in sorting when output to stdout (by Peter Chines)
Heng Li [Fri, 9 Jul 2010 21:05:10 +0000 (21:05 +0000)]
change the command line option of pileup
Heng Li [Fri, 9 Jul 2010 04:39:34 +0000 (04:39 +0000)]
make pileup work with CIGAR with I/D at the beginning or in the end
Heng Li [Fri, 9 Jul 2010 02:36:12 +0000 (02:36 +0000)]
* make tview more friendly
* a temporary remedy for an issue in indel calling
Heng Li [Thu, 8 Jul 2010 18:43:52 +0000 (18:43 +0000)]
* samtools-0.1.7-r607
* improved the genotype accuracy for indels
* use the SOAPsnp model for SNP calling by default.
Heng Li [Thu, 8 Jul 2010 05:05:19 +0000 (05:05 +0000)]
removed a debugging example
Heng Li [Thu, 8 Jul 2010 05:04:09 +0000 (05:04 +0000)]
* samtools-.1.7-18 (r605)
* fixed an issue when a deletion and mismatch occur at the same time
and the base quality is higher than 40 (if -I40).
Heng Li [Fri, 2 Jul 2010 23:32:24 +0000 (23:32 +0000)]
fixed a minor bug in idxstats
Heng Li [Wed, 16 Jun 2010 13:03:59 +0000 (13:03 +0000)]
fixed a minor bug in indexing
Heng Li [Tue, 15 Jun 2010 14:17:53 +0000 (14:17 +0000)]
change printf() to puts in exporting
Heng Li [Mon, 14 Jun 2010 01:41:11 +0000 (01:41 +0000)]
minor fix. No actual effect.
Heng Li [Mon, 14 Jun 2010 01:32:45 +0000 (01:32 +0000)]
added Makefile targets to compile shared/dynamic library
Heng Li [Sun, 13 Jun 2010 23:48:07 +0000 (23:48 +0000)]
* samtools-0.1.7-17 (r596)
* also keep the number of coor-less reads in the index file
Heng Li [Sun, 13 Jun 2010 22:54:26 +0000 (22:54 +0000)]
* samtools-0.1.7-16 (r595)
* write additional information to bam index
Heng Li [Sun, 13 Jun 2010 21:29:52 +0000 (21:29 +0000)]
fixed a bug for unmapped sequences in indexing
Heng Li [Sat, 12 Jun 2010 22:11:32 +0000 (22:11 +0000)]
rename iterf as iter
Heng Li [Sat, 12 Jun 2010 22:02:38 +0000 (22:02 +0000)]
* samtools-0.1.7-15 (r592)
* fixed a few minor memory leaks in the new pileup code
* improved the functionality of mpileup
Heng Li [Sat, 12 Jun 2010 18:09:22 +0000 (18:09 +0000)]
* samtools-0.1.7-14 (r591)
* elementary multi-way pileup. More testing and more functionality to be done.
Heng Li [Sat, 12 Jun 2010 05:00:24 +0000 (05:00 +0000)]
* samtools-0.1.7-13 (r590)
* added mpileup APIs. No compiling errors, but not tested at all. It is late.
Heng Li [Sat, 12 Jun 2010 02:37:09 +0000 (02:37 +0000)]
* samtools-0.1.7-12 (r589)
* added iterator-like APIs for pileup
Heng Li [Fri, 11 Jun 2010 21:41:13 +0000 (21:41 +0000)]
* samtools-0.1.7-11 (r588)
* ported a few improvements from tabix back to samtools
Heng Li [Fri, 11 Jun 2010 21:33:16 +0000 (21:33 +0000)]
* samtools-0.1.7-10 (r587)
* added iterator interface for bam_fetch (ported back from tabix)
Heng Li [Fri, 11 Jun 2010 17:23:53 +0000 (17:23 +0000)]
* samtools-0.1.7-9 (r586)
* added "reheader" to replace the BAM header
Heng Li [Fri, 11 Jun 2010 16:22:06 +0000 (16:22 +0000)]
* samtools-0.1.7-8 (r585)
* speed up "view"
Heng Li [Fri, 11 Jun 2010 16:00:41 +0000 (16:00 +0000)]
* samtools-0.1.7-7 (r584)
* ported tabix BGZF to samtools
* flush BGZF after writing the BAM header and between alignment boundaries
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).