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14 years agoadded an alternative prior
Heng Li [Fri, 23 Jul 2010 17:25:44 +0000 (17:25 +0000)]
added an alternative prior

14 years agocalculate posterior allele frequency
Heng Li [Fri, 23 Jul 2010 15:48:51 +0000 (15:48 +0000)]
calculate posterior allele frequency

14 years ago * samtools-0.1.8-3 (r627)
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.

14 years ago * preliminary multisample SNP caller.
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

14 years ago * samtools-0.1.8-2 (r617)
Heng Li [Wed, 14 Jul 2010 20:26:27 +0000 (20:26 +0000)]
 * samtools-0.1.8-2 (r617)
 * allele frequency calculation apparently works...

14 years ago * added mutli-sample framework. It is not working, yet.
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

14 years ago * samtools-0.1.8-1 (r615)
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

14 years agoRelease samtools-0.1.8
Heng Li [Mon, 12 Jul 2010 02:40:56 +0000 (02:40 +0000)]
Release samtools-0.1.8

14 years agofixed a compiling issue for Windows
Heng Li [Mon, 12 Jul 2010 01:08:56 +0000 (01:08 +0000)]
fixed a compiling issue for Windows

14 years agofixed a bug in sorting when output to stdout (by Peter Chines)
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)

14 years agochange the command line option of pileup
Heng Li [Fri, 9 Jul 2010 21:05:10 +0000 (21:05 +0000)]
change the command line option of pileup

14 years agomake pileup work with CIGAR with I/D at the beginning or in the end
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

14 years ago * make tview more friendly
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

14 years ago * samtools-0.1.7-r607
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.

14 years agoremoved a debugging example
Heng Li [Thu, 8 Jul 2010 05:05:19 +0000 (05:05 +0000)]
removed a debugging example

14 years ago * samtools-.1.7-18 (r605)
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).

14 years agofixed a minor bug in idxstats
Heng Li [Fri, 2 Jul 2010 23:32:24 +0000 (23:32 +0000)]
fixed a minor bug in idxstats

14 years agofixed a minor bug in indexing
Heng Li [Wed, 16 Jun 2010 13:03:59 +0000 (13:03 +0000)]
fixed a minor bug in indexing

14 years agochange printf() to puts in exporting
Heng Li [Tue, 15 Jun 2010 14:17:53 +0000 (14:17 +0000)]
change printf() to puts in exporting

14 years agominor fix. No actual effect.
Heng Li [Mon, 14 Jun 2010 01:41:11 +0000 (01:41 +0000)]
minor fix. No actual effect.

14 years agoadded Makefile targets to compile shared/dynamic library
Heng Li [Mon, 14 Jun 2010 01:32:45 +0000 (01:32 +0000)]
added Makefile targets to compile shared/dynamic library

14 years ago * samtools-0.1.7-17 (r596)
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

14 years ago * samtools-0.1.7-16 (r595)
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

14 years agofixed a bug for unmapped sequences in indexing
Heng Li [Sun, 13 Jun 2010 21:29:52 +0000 (21:29 +0000)]
fixed a bug for unmapped sequences in indexing

14 years agorename iterf as iter
Heng Li [Sat, 12 Jun 2010 22:11:32 +0000 (22:11 +0000)]
rename iterf as iter

14 years ago * samtools-0.1.7-15 (r592)
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

14 years ago * samtools-0.1.7-14 (r591)
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.

14 years ago * samtools-0.1.7-13 (r590)
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.

14 years ago * samtools-0.1.7-12 (r589)
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

14 years ago * samtools-0.1.7-11 (r588)
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

14 years ago * samtools-0.1.7-10 (r587)
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)

14 years ago * samtools-0.1.7-9 (r586)
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

14 years ago * samtools-0.1.7-8 (r585)
Heng Li [Fri, 11 Jun 2010 16:22:06 +0000 (16:22 +0000)]
 * samtools-0.1.7-8 (r585)
 * speed up "view"

14 years ago * samtools-0.1.7-7 (r584)
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

14 years agoInitial release on behalf of Aylwyn Scally
Petr Danecek [Fri, 11 Jun 2010 15:58:20 +0000 (15:58 +0000)]
Initial release on behalf of Aylwyn Scally

14 years agoAdded a note about the indels coordinates
Petr Danecek [Fri, 7 May 2010 12:41:56 +0000 (12:41 +0000)]
Added a note about the indels coordinates

14 years agoAdded the possibility to print or not to print the reference allele
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

14 years agoMore descriptive message for space separated tags
Petr Danecek [Thu, 15 Apr 2010 08:33:55 +0000 (08:33 +0000)]
More descriptive message for space separated tags

14 years agoSpeedup with -i, no need to query the reference all the time
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

14 years agoFixed the order of sequences in the header
Petr Danecek [Mon, 15 Mar 2010 14:03:51 +0000 (14:03 +0000)]
Fixed the order of sequences in the header

14 years agoAdded possibility to select indels only and fixed a bug in reporting homozygous indels.
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.

14 years agoImprove the invalid 'BAM\1' magic number error message, and also print it
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.

14 years agoImproved efficiency of header parsing
Petr Danecek [Fri, 26 Feb 2010 15:51:40 +0000 (15:51 +0000)]
Improved efficiency of header parsing

14 years agoUpdated export2sam.pl by Chris Saunders from Illumina.
Heng Li [Wed, 24 Feb 2010 02:08:48 +0000 (02:08 +0000)]
Updated export2sam.pl by Chris Saunders from Illumina.

14 years agoFixed filtering of SNPs near indels. Added min indel and SNP quality filter.
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.

14 years agoPrint an error for pileups in simple format
Petr Danecek [Fri, 12 Feb 2010 09:52:37 +0000 (09:52 +0000)]
Print an error for pileups in simple format

14 years agoadded a hidden option in pileup to output the base position (for Erin)
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)

14 years agoAdded possibility to specify a custom column title for the data column
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

14 years agoAdded the -d option to limit maximum depth for indels.
Petr Danecek [Tue, 9 Feb 2010 14:46:09 +0000 (14:46 +0000)]
Added the -d option to limit maximum depth for indels.

14 years agoAdded VCF header
Petr Danecek [Wed, 3 Feb 2010 12:57:27 +0000 (12:57 +0000)]
Added VCF header

14 years ago * samtools-0.1.7-6
Heng Li [Mon, 1 Feb 2010 14:13:19 +0000 (14:13 +0000)]
 * samtools-0.1.7-6
 * fixed a bug in faidx

14 years agoPut the right filename in the error message.
On behalf of John Marshall [Mon, 11 Jan 2010 23:51:49 +0000 (23:51 +0000)]
Put the right filename in the error message.

14 years ago * samtools-0.1.7-5 (r528)
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

14 years agoFixed a bug in knet_seek
Petr Danecek [Fri, 11 Dec 2009 17:31:05 +0000 (17:31 +0000)]
Fixed a bug in knet_seek

14 years agoSmall fix in VCF format: dot for the empty INFO field
Petr Danecek [Fri, 11 Dec 2009 12:51:18 +0000 (12:51 +0000)]
Small fix in VCF format: dot for the empty INFO field

14 years agoAllow tabs in the CO header field
Petr Danecek [Fri, 11 Dec 2009 09:36:18 +0000 (09:36 +0000)]
Allow tabs in the CO header field

14 years agoDepend on libbam.a rather than the phony target, so that samtools is not
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.

14 years agoFix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
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.

14 years ago * samtools-0.1.7-4 (r522)
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

14 years ago * samtools-0.1.7-3 (r521)
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

14 years ago * samtools-0.1.7-2 (r520)
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)

14 years agoPut libraries at the end, so they can resolve references from libbam.a
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.

14 years agoAlso clean *.exe (for Cygwin users using this makefile).
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).

14 years agoIndex files should be opened in binary mode, not text mode.
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.

14 years agoanother example program
Heng Li [Fri, 27 Nov 2009 20:18:59 +0000 (20:18 +0000)]
another example program

14 years ago * samtools-0.1.7-1 (r515)
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

14 years agoFormat 'c'-encoded auxiliary fields correctly, as *signed* integers.
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.

14 years agoUpdate Makefile.mingw for the same reason
Heng Li [Mon, 16 Nov 2009 15:13:07 +0000 (15:13 +0000)]
Update Makefile.mingw for the same reason

14 years agoFixed a bug in compiling razip
Heng Li [Mon, 16 Nov 2009 15:00:08 +0000 (15:00 +0000)]
Fixed a bug in compiling razip

14 years agoRelease samtools-0.1.7 (r510)
Heng Li [Tue, 10 Nov 2009 15:55:41 +0000 (15:55 +0000)]
Release samtools-0.1.7 (r510)

14 years ago * samtools-0.1.6-22 (r509)
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

14 years ago * samtools-0.1.6-21 (r508)
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

15 years ago * samtools-0.1.6-19 (r494)
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

15 years ago * samtools-0.1.6-18 (r493)
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

15 years agoAdded sam_header_line_free call for sam_header_parse2
Petr Danecek [Sat, 24 Oct 2009 13:43:25 +0000 (13:43 +0000)]
Added sam_header_line_free call for sam_header_parse2

15 years ago * BUGGY VERSION
Heng Li [Sat, 24 Oct 2009 04:50:16 +0000 (04:50 +0000)]
 * BUGGY VERSION
 * fixed a minor bug

15 years ago * BUGGY VERSION
Heng Li [Sat, 24 Oct 2009 04:45:12 +0000 (04:45 +0000)]
 * BUGGY VERSION
 * improved the interface a bit
 * bug unfixed

15 years ago * BUGGY VERSION. Please NOT use it.
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.

15 years ago * This revision is SERIOUSLY BUGGY. Please NOT use it.
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

15 years agoNow possible to merge multiple HeaderDict dictionaries
Petr Danecek [Fri, 23 Oct 2009 15:44:32 +0000 (15:44 +0000)]
Now possible to merge multiple HeaderDict dictionaries

15 years ago(no commit message)
Petr Danecek [Thu, 22 Oct 2009 15:46:58 +0000 (15:46 +0000)]

15 years ago(no commit message)
Petr Danecek [Thu, 22 Oct 2009 15:41:56 +0000 (15:41 +0000)]

15 years ago * samtools-0.1.6-17 (r484)
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/

15 years ago * samtools-0.1.6-16 (r483)
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.

15 years ago * samtools-0.1.6-15 (r482)
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

15 years ago * samtools-0.1.6-14 (r480)
Heng Li [Sun, 18 Oct 2009 04:07:21 +0000 (04:07 +0000)]
 * samtools-0.1.6-14 (r480)
 * rmdup is now RG aware

15 years agoadded a small unitity to parse SRA XML files
Heng Li [Sun, 18 Oct 2009 02:05:20 +0000 (02:05 +0000)]
added a small unitity to parse SRA XML files

15 years ago * samtools-0.1.6-13 (r479)
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

15 years ago * samtools-0.1.6-12 (r478)
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

15 years ago * samtools-0.1.6-11 (r477)
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)

15 years agoAdded the sam2vcf.pl script.
Petr Danecek [Fri, 9 Oct 2009 15:45:36 +0000 (15:45 +0000)]
Added the sam2vcf.pl script.

15 years agoUnfinished modification. Please do not use this revision...
Heng Li [Thu, 8 Oct 2009 14:19:16 +0000 (14:19 +0000)]
Unfinished modification. Please do not use this revision...

15 years agoRemoved the offending knet_seek message.
Petr Danecek [Thu, 8 Oct 2009 10:39:54 +0000 (10:39 +0000)]
Removed the offending knet_seek message.

15 years agoBug fix - faidx on RAZF compressed files now working.
Petr Danecek [Tue, 6 Oct 2009 13:26:35 +0000 (13:26 +0000)]
Bug fix - faidx on RAZF compressed files now working.

15 years agoClarify the meaning of a region like "chr2:1,000,000".
Heng Li [Fri, 2 Oct 2009 12:42:57 +0000 (12:42 +0000)]
Clarify the meaning of a region like "chr2:1,000,000".

15 years agoFixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
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)

15 years ago * samtools-0.1.6-9 (r470)
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)

15 years ago * samtools-0.1.6-9 (r469)
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.

15 years ago * samtools-0.1.6-7 (r468)
Heng Li [Mon, 28 Sep 2009 09:18:29 +0000 (09:18 +0000)]
 * samtools-0.1.6-7 (r468)
 * make merge stable

15 years agoChanged the mode for newly created files to 0666. This allows less strict permissions...
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).