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git.donarmstrong.com Git - samtools.git/log
peterjc [Tue, 3 Apr 2012 11:05:17 +0000 (12:05 +0100)]
Minimal 'samtools depad' command line parsing (-? only so far)
peterjc [Tue, 3 Apr 2012 10:51:41 +0000 (11:51 +0100)]
Adding a usage function to 'samtools depad' following 'samtools view' style
peterjc [Mon, 2 Apr 2012 10:30:36 +0000 (11:30 +0100)]
Add a tiny bit of help text to 'samtools depad' command.
peterjc [Mon, 2 Apr 2012 10:26:27 +0000 (11:26 +0100)]
Revert one of my earlier changes - Heng was right, CIGAR P not sensible in a padded reference
peterjc [Mon, 2 Apr 2012 10:22:17 +0000 (11:22 +0100)]
Fix buffer overflow in 'samtools depad' with CIGAR D operators
peterjc [Fri, 30 Mar 2012 16:39:32 +0000 (17:39 +0100)]
Fixed the next silly error on that line.
peterjc [Fri, 30 Mar 2012 16:35:38 +0000 (17:35 +0100)]
Fix silly typo
peterjc [Fri, 30 Mar 2012 16:32:46 +0000 (17:32 +0100)]
More elegant solution to avoid superfluous leading P ops
peterjc [Fri, 30 Mar 2012 16:16:12 +0000 (17:16 +0100)]
Refine logic for removing superfluous P ops (still testing ...)
Petr Danecek [Tue, 12 Jun 2012 15:18:12 +0000 (16:18 +0100)]
Merge remote branch 'rq/getopt_mac'
peterjc [Tue, 12 Jun 2012 14:50:19 +0000 (15:50 +0100)]
Fix missing declaration for getopt on Mac OS X
kortschak [Thu, 7 Jun 2012 22:16:26 +0000 (07:46 +0930)]
Update bam1_core_t and bam1_t documentation
* Query strand is no longer represented by a field of its own.
* The order of segments in data appears to have changed.
* Added notes about encoding of cigar and seq data in the bam1_t.data byte array.
Petr Danecek [Thu, 7 Jun 2012 11:24:28 +0000 (12:24 +0100)]
New -s option for multisample BAMs: include only reads from a given sample in the display
Petr Danecek [Wed, 30 May 2012 09:20:51 +0000 (10:20 +0100)]
Petr Danecek [Fri, 25 May 2012 13:16:25 +0000 (14:16 +0100)]
The -E switch to recalculate extended BAQ on the fly, ignoring existing BQs
Petr Danecek [Fri, 25 May 2012 07:41:01 +0000 (08:41 +0100)]
Fix to prevent long stretches of Ns to be mistaken for indels; Always output the most likely ALT allele
Petr Danecek [Fri, 18 May 2012 09:38:07 +0000 (10:38 +0100)]
Merge branch 'master' of github.com:samtools/samtools
Petr Danecek [Fri, 18 May 2012 09:37:58 +0000 (10:37 +0100)]
Added -f, -F options. Count and plot indels per cycle for each mate pair separately.
Heng Li [Thu, 17 May 2012 20:12:36 +0000 (16:12 -0400)]
change the default clevel to 1 for speed
Heng Li [Thu, 17 May 2012 20:06:09 +0000 (16:06 -0400)]
added bamshuf from htslib
Heng Li [Fri, 11 May 2012 02:03:54 +0000 (22:03 -0400)]
bugfix: bgzf-mt may write prematured output
Heng Li [Sat, 5 May 2012 15:31:20 +0000 (11:31 -0400)]
added length threshold
Petr Danecek [Thu, 3 May 2012 09:26:18 +0000 (10:26 +0100)]
Reverted to the previous behaviour, the unmapped reads are not removed. Added -r switch for backward compatibility.
Petr Danecek [Tue, 24 Apr 2012 08:51:47 +0000 (09:51 +0100)]
init_regions: check for non-matching sequence names
Petr Danecek [Mon, 23 Apr 2012 19:07:13 +0000 (20:07 +0100)]
Resolved merge conflict
Petr Danecek [Mon, 23 Apr 2012 18:55:38 +0000 (19:55 +0100)]
Indexed access can be now combined with target regions. The number of mapped bases more accurate now with -t.
Heng Li [Tue, 17 Apr 2012 20:03:11 +0000 (16:03 -0400)]
r572: added "bedcov" command
Heng Li [Tue, 17 Apr 2012 18:34:58 +0000 (14:34 -0400)]
change getline() to mygetline()
Heng Li [Tue, 17 Apr 2012 18:34:45 +0000 (14:34 -0400)]
updated to the latest kseq
Petr Danecek [Thu, 12 Apr 2012 19:15:38 +0000 (20:15 +0100)]
Added check for out-of-bounds indels at the end of reads
Petr Danecek [Thu, 12 Apr 2012 17:48:17 +0000 (18:48 +0100)]
On behalf of Bradford Powell: fixed typo in VCF header, output DV not DP
Petr Danecek [Wed, 4 Apr 2012 10:01:49 +0000 (11:01 +0100)]
Removed glibc dependency (getline)
Petr Danecek [Wed, 4 Apr 2012 09:07:27 +0000 (10:07 +0100)]
Merge remote branch 'main/master'
Conflicts:
misc/Makefile
misc/bamcheck.c
Heng Li [Tue, 3 Apr 2012 16:23:35 +0000 (12:23 -0400)]
Merge branch 'master' of github.com:samtools/samtools
Heng Li [Tue, 3 Apr 2012 16:23:14 +0000 (12:23 -0400)]
compiling errors on some machines
Petr Danecek [Mon, 2 Apr 2012 11:40:37 +0000 (12:40 +0100)]
Temporary fix to prevent segfault in kpa_glocal
Heng Li [Fri, 30 Mar 2012 02:27:57 +0000 (22:27 -0400)]
shrink bam1_t::m_data when sorting
Otherwise most of allocated memory may not be used
Heng Li [Thu, 29 Mar 2012 18:05:37 +0000 (14:05 -0400)]
Merge branch 'master' of github.com:samtools/samtools into mt
Conflicts:
misc/Makefile
Also, killed warnings on Mac
samtools [Thu, 29 Mar 2012 17:57:02 +0000 (10:57 -0700)]
Merge pull request #2 from peterjc/depad
Improvments to 'samtools depad' command
Petr Danecek [Thu, 29 Mar 2012 09:50:16 +0000 (17:50 +0800)]
Compile cleanly from top-level Makefile. Check for out of bounds tids.
Petr Danecek [Thu, 29 Mar 2012 09:50:16 +0000 (10:50 +0100)]
Compile cleanly from top-level Makefile. Check for out of bounds tids.
Petr Danecek [Wed, 28 Mar 2012 09:04:40 +0000 (17:04 +0800)]
Added rule for bamcheck creation
Petr Danecek [Wed, 28 Mar 2012 09:04:40 +0000 (10:04 +0100)]
Added rule for bamcheck creation
Petr Danecek [Tue, 27 Mar 2012 13:49:59 +0000 (21:49 +0800)]
Initial release of bamcheck and plot-bamcheck
Petr Danecek [Tue, 27 Mar 2012 13:49:59 +0000 (14:49 +0100)]
Initial release of bamcheck and plot-bamcheck
peterjc [Mon, 26 Mar 2012 14:57:46 +0000 (15:57 +0100)]
Check reference length in BAM header against embedded reference in 'samtools depad'
peterjc [Mon, 26 Mar 2012 14:35:44 +0000 (15:35 +0100)]
Cope with trailing CIGAR H (or S and H) in 'samtools depad'
peterjc [Mon, 26 Mar 2012 14:28:49 +0000 (15:28 +0100)]
Cope with leading CIGAR H (or H and S) in 'samtools depad'
peterjc [Mon, 26 Mar 2012 14:22:15 +0000 (15:22 +0100)]
Tolerate CIGAR H operators in 'samtools depad'
peterjc [Mon, 26 Mar 2012 14:07:17 +0000 (15:07 +0100)]
Include leading CIGAR P operators in 'samtools depad'
peterjc [Mon, 26 Mar 2012 13:23:37 +0000 (14:23 +0100)]
Record actual sequence in unpad_seq (fixes apparently harmless bug)
Heng Li [Sat, 24 Mar 2012 21:32:45 +0000 (17:32 -0400)]
filter on query sequence length (not aln len)
Heng Li [Sat, 24 Mar 2012 00:42:23 +0000 (20:42 -0400)]
move seqtk to a separate project
peterjc [Fri, 23 Mar 2012 16:59:53 +0000 (16:59 +0000)]
Correct my error message; assed some comments
peterjc [Fri, 23 Mar 2012 13:04:05 +0000 (13:04 +0000)]
Add TODO note about reference lengths
peterjc [Fri, 23 Mar 2012 12:51:32 +0000 (12:51 +0000)]
Cope with CIGAR D or P to mark gaps in an embedded padded reference
peterjc [Thu, 22 Mar 2012 17:49:40 +0000 (17:49 +0000)]
Check current reference sequence matches RNAME in samtools depad
peterjc [Thu, 22 Mar 2012 17:49:15 +0000 (17:49 +0000)]
Support CIGAR X/= in depad
peterjc [Thu, 22 Mar 2012 17:48:47 +0000 (17:48 +0000)]
Helpful error message on bad CIGAR in unpad_seq
Heng Li [Thu, 22 Mar 2012 01:54:01 +0000 (21:54 -0400)]
change SO
Heng Li [Thu, 22 Mar 2012 00:48:34 +0000 (20:48 -0400)]
a little more accurate mem estimate
Heng Li [Thu, 22 Mar 2012 00:39:15 +0000 (20:39 -0400)]
control compression level at command line
Heng Li [Tue, 20 Mar 2012 18:25:48 +0000 (14:25 -0400)]
optionally surpress /[12] in bam2fq
Heng Li [Tue, 20 Mar 2012 15:49:52 +0000 (11:49 -0400)]
Merge branch 'master' into mt
Heng Li [Tue, 20 Mar 2012 15:49:29 +0000 (11:49 -0400)]
bugfix: downsampling not always working
Heng Li [Mon, 19 Mar 2012 18:11:30 +0000 (14:11 -0400)]
name sorting checkes READ1 and READ2
Heng Li [Mon, 19 Mar 2012 17:37:30 +0000 (13:37 -0400)]
sorting also considers strand
Previously, merging considers strand but sorting not. This is a bug and breaks
stability. Now it seems that sorting is stable and it gives the same output no
matter what parameters in use.
Heng Li [Sun, 18 Mar 2012 21:36:26 +0000 (17:36 -0400)]
change the default block size in sorting
Heng Li [Sun, 18 Mar 2012 21:15:30 +0000 (17:15 -0400)]
multi-threaded sorting
Heng Li [Sun, 18 Mar 2012 18:46:49 +0000 (14:46 -0400)]
added .gitignore
Heng Li [Sun, 18 Mar 2012 18:46:00 +0000 (14:46 -0400)]
added mt comression to merge
Heng Li [Sun, 18 Mar 2012 18:31:45 +0000 (14:31 -0400)]
updated the alphanum comparison function
Heng Li [Sun, 18 Mar 2012 18:12:45 +0000 (14:12 -0400)]
avoid wasting CPU time by the master thread
Heng Li [Sun, 18 Mar 2012 17:51:16 +0000 (13:51 -0400)]
use conditional variable
Heng Li [Sun, 18 Mar 2012 16:12:23 +0000 (12:12 -0400)]
bugfix in caching
Heng Li [Sun, 18 Mar 2012 15:43:30 +0000 (11:43 -0400)]
multi-threading working on toy examples
Heng Li [Sun, 18 Mar 2012 05:23:55 +0000 (01:23 -0400)]
preliminary implementation; not tested
Heng Li [Sun, 18 Mar 2012 03:16:54 +0000 (23:16 -0400)]
updated with the latest bgzf library
Heng Li [Fri, 9 Mar 2012 03:25:34 +0000 (22:25 -0500)]
On behalf of Petr: multi-allelic GT
Heng Li [Fri, 9 Mar 2012 02:47:29 +0000 (02:47 +0000)]
Removed SVN ChangeLog; merged my private github Log to ChangeLog.old
Heng Li [Fri, 9 Mar 2012 02:43:02 +0000 (02:43 +0000)]
doc for downsampling
Heng Li [Fri, 9 Mar 2012 02:39:49 +0000 (02:39 +0000)]
another example, used by g1k for QA
Heng Li [Fri, 9 Mar 2012 02:39:19 +0000 (02:39 +0000)]
Two auxilary Lua scripts
Heng Li [Fri, 9 Mar 2012 02:31:51 +0000 (02:31 +0000)]
Incoporated changes from Nils Homer.
* Better error checking in bam_sort.c
* Parse "K", "M" and "G" in the sort command
* Better color-space handling
* Bugfix of wrong integer conversion
New commands are not added.
Heng Li [Thu, 16 Feb 2012 14:33:07 +0000 (14:33 +0000)]
bugfix: wrong SP; missing DV in the VCF header
Heng Li [Wed, 8 Feb 2012 16:37:40 +0000 (16:37 +0000)]
changes from git
Heng Li [Wed, 28 Sep 2011 05:36:36 +0000 (05:36 +0000)]
unpadded output
Heng Li [Fri, 23 Sep 2011 15:20:15 +0000 (15:20 +0000)]
added the ace2sam converter
Heng Li [Fri, 23 Sep 2011 15:14:21 +0000 (15:14 +0000)]
converted padded SAM to unpadded SAM
Heng Li [Fri, 2 Sep 2011 16:57:34 +0000 (16:57 +0000)]
* Updated samtools to the latest
* Added seqtk.c
* Updated wgsim.c
* release samtools-0.1.18
Heng Li [Wed, 17 Aug 2011 18:26:22 +0000 (18:26 +0000)]
* bugfix in index: large memory when a read pos is 1
* bugfix in BAQ: incorrect probability (rare)
* compute variant distance bias (commited by Petr)
* bugfix for computing LRT2: LRT2=nan
Heng Li [Fri, 15 Jul 2011 20:04:59 +0000 (20:04 +0000)]
allow to set seed in view-subsampling
Heng Li [Fri, 15 Jul 2011 19:56:04 +0000 (19:56 +0000)]
subsampling read pairs
Heng Li [Wed, 13 Jul 2011 13:50:16 +0000 (13:50 +0000)]
support trio indels
Heng Li [Thu, 7 Jul 2011 04:37:01 +0000 (04:37 +0000)]
for WIN32 compatibility
Heng Li [Thu, 7 Jul 2011 03:46:12 +0000 (03:46 +0000)]
fixed a bug in bam_plcmd.c
Heng Li [Thu, 7 Jul 2011 02:59:05 +0000 (02:59 +0000)]
Release samtools-0.1.17
Heng Li [Wed, 15 Jun 2011 15:08:41 +0000 (15:08 +0000)]
fixed a bug caused by a recent patch
Heng Li [Fri, 3 Jun 2011 18:49:27 +0000 (18:49 +0000)]
* 0.1.16-dev (r969:252)
* faidx/view: smarter way to parse a region string
* index: more rigorously check the sorting order
* Makefile: added -s to ar
* bcftools: compute 2-degree P-value by default
* bcftools: compute the ML estimate of the allele count
Heng Li [Fri, 22 Apr 2011 13:46:42 +0000 (13:46 +0000)]
Removed the pileup command