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git.donarmstrong.com Git - samtools.git/log
Petr Danecek [Fri, 15 Mar 2013 08:40:35 +0000 (08:40 +0000)]
mpileup: New HWE, QBD, RPS annotations. Modified VDB (beware: this version of VDB may be broken). Fix in indel calling: Ignore insertions with N's. Output contigs in the VCF header. New sam_header2tbl_n() API call.
Petr Danecek [Tue, 12 Mar 2013 13:25:17 +0000 (13:25 +0000)]
Merge remote branch 'remotes/master/master' into fb-annots
Petr Danecek [Tue, 12 Mar 2013 13:24:16 +0000 (13:24 +0000)]
backup commit
Petr Danecek [Tue, 12 Mar 2013 13:17:26 +0000 (13:17 +0000)]
Merge branch 'master' of github.com:samtools/samtools
Petr Danecek [Tue, 12 Mar 2013 13:06:52 +0000 (13:06 +0000)]
bcftools view: Exit with an error if the -l file cannot be read
Heng Li [Sun, 10 Mar 2013 00:12:41 +0000 (16:12 -0800)]
Merge pull request #30 from leecbaker/master
Fixed several small memory leaks.
Lee Baker [Sat, 9 Mar 2013 19:27:56 +0000 (13:27 -0600)]
Fix memory leaks:
* When downloading a remote FASTA index
* When indexing a BAM, we can't open the FAI file
* When indexing a BCF, we can't open the index file
* Parsing a VCF header with no sample line
* Encountering multiple adjacent tabs in a SAM header
Petr Danecek [Thu, 7 Mar 2013 19:21:43 +0000 (19:21 +0000)]
backup commit
Petr Danecek [Fri, 1 Mar 2013 13:14:32 +0000 (13:14 +0000)]
bcftools view: always output the header, even when no other arguments are given
Manuel Holtgrewe [Wed, 27 Feb 2013 13:05:24 +0000 (14:05 +0100)]
Adding -f flag to samtools sort to give output name directly.
Petr Danecek [Mon, 28 Jan 2013 09:07:23 +0000 (09:07 +0000)]
Merge remote branch 'remotes/pierre/master' into develop
lindenb [Fri, 25 Jan 2013 14:29:08 +0000 (15:29 +0100)]
fix html
lindenb [Fri, 25 Jan 2013 14:18:57 +0000 (15:18 +0100)]
cont
lindenb [Fri, 25 Jan 2013 14:12:12 +0000 (15:12 +0100)]
works
lindenb [Fri, 25 Jan 2013 13:03:29 +0000 (14:03 +0100)]
cont
lindenb [Fri, 25 Jan 2013 08:08:19 +0000 (09:08 +0100)]
works with curses
Pierre Lindenbaum [Fri, 25 Jan 2013 07:14:22 +0000 (08:14 +0100)]
cont
Pierre Lindenbaum [Thu, 24 Jan 2013 20:40:40 +0000 (21:40 +0100)]
...
Heng Li [Mon, 7 Jan 2013 16:59:49 +0000 (11:59 -0500)]
dump log-likelihood
Petr Danecek [Thu, 3 Jan 2013 14:04:47 +0000 (14:04 +0000)]
bamcheck: new stats, number of filtered vs raw sequences
Petr Danecek [Thu, 13 Dec 2012 07:49:32 +0000 (07:49 +0000)]
Merge branch 'vsbuffalo-master' into develop
Vince Buffalo [Thu, 13 Dec 2012 07:15:19 +0000 (23:15 -0800)]
fixed missing braces
Vince Buffalo [Thu, 13 Dec 2012 03:39:22 +0000 (19:39 -0800)]
big fix: using samtools view file.bam gibberish returns alignments; iter not checked against kh_end
Petr Danecek [Wed, 12 Dec 2012 13:15:41 +0000 (13:15 +0000)]
mpileup: New --rf and --ff options for filtering reads
Petr Danecek [Wed, 12 Dec 2012 13:13:55 +0000 (13:13 +0000)]
bamcheck: New stats - the number of QC failed reads and non-primary alignments
Petr Danecek [Wed, 12 Dec 2012 13:13:10 +0000 (13:13 +0000)]
bam2depth: Enabled reading the list of BAMs from a file list
Petr Danecek [Tue, 11 Dec 2012 07:55:29 +0000 (07:55 +0000)]
ksort.h: declared __ks_insertsort_##name as static to compile with C99. (On behalf of Hanspeter Niederstrasser.)
Petr Danecek [Mon, 3 Dec 2012 10:00:44 +0000 (10:00 +0000)]
bam_plcmd.c: more descriptive -b usage help message
Petr Danecek [Mon, 3 Dec 2012 09:14:47 +0000 (09:14 +0000)]
bam_plcmd.c: added sanity check in read_file_list, complain if file list is not a file list
Petr Danecek [Mon, 3 Dec 2012 09:13:21 +0000 (09:13 +0000)]
bamcheck: New stats, number of pairs mapped to different chromosomes
Petr Danecek [Tue, 27 Nov 2012 13:36:14 +0000 (13:36 +0000)]
misc/Makefile, on behalf of ghuls: changed the order of bamcheck rules with -lz last
Petr Danecek [Tue, 27 Nov 2012 10:45:30 +0000 (10:45 +0000)]
bamcheck: max quality value increased to 255 to handle missing qual field; pairs with IS=0 can still count as paired; output IS=0 stats as well
Petr Danecek [Thu, 22 Nov 2012 09:58:39 +0000 (09:58 +0000)]
bamcheck: Fixed a bug introduced by previous change igcd to uint: not a good idea to init with -1.
Petr Danecek [Thu, 15 Nov 2012 09:15:43 +0000 (09:15 +0000)]
Merge remote branch 'remotes/pd3master/master' into develop
Petr Danecek [Fri, 9 Nov 2012 11:59:42 +0000 (11:59 +0000)]
Drop empty bins from coverage distribution
Petr Danecek [Fri, 9 Nov 2012 11:50:05 +0000 (11:50 +0000)]
Changed default reflen; more informative error message when GCD bin size too small or reflen too big
Petr Danecek [Thu, 11 Oct 2012 11:11:16 +0000 (12:11 +0100)]
More user-friendly error output
Petr Danecek [Wed, 10 Oct 2012 11:47:41 +0000 (12:47 +0100)]
Complain when BAM cannot be open. Severe bug fixed in -m haploid calling.
Petr Danecek [Wed, 12 Sep 2012 14:45:30 +0000 (15:45 +0100)]
Merge remote branch 'remotes/pd3/master'
Conflicts:
misc/bamcheck.c
Petr Danecek [Wed, 5 Sep 2012 15:36:24 +0000 (16:36 +0100)]
Fix in insertion cycle calculation of rev reads
Petr Danecek [Wed, 5 Sep 2012 10:07:49 +0000 (11:07 +0100)]
GC-depth calculation now more robust to small GCD bin sizes
Petr Danecek [Tue, 4 Sep 2012 08:09:19 +0000 (09:09 +0100)]
New --GC-depth option to bamcheck. Take into account not so frequent CIGAR codes. Fix in realloc_buffers. Prevent segfault with long command line options; Set xrange correctly in plot-bamcheck coverage.gp
Heng Li [Tue, 21 Aug 2012 14:25:04 +0000 (07:25 -0700)]
Merge pull request #14 from peterjc/depad3
Update MPOS/PNEXT during 'samtools depad'
peterjc [Fri, 17 Aug 2012 10:28:27 +0000 (11:28 +0100)]
Fix 'samtools depad' seg-fault when MPOS/PNEXT given but MRNM/RNEXT is not
peterjc [Wed, 20 Jun 2012 15:48:43 +0000 (16:48 +0100)]
Tweak order free things (avoids an 'samtools depad' seg fault on error)
peterjc [Wed, 20 Jun 2012 15:16:54 +0000 (16:16 +0100)]
First attempt at updating MPOS in 'samtools depad'
Heng Li [Fri, 3 Aug 2012 18:46:23 +0000 (14:46 -0400)]
r580: bugfix - bam_aux_get() error given 'f' type
Petr Danecek [Thu, 2 Aug 2012 13:33:45 +0000 (14:33 +0100)]
Use int64_t to prevent count overflow in view -c; on behalf of Joshua Randall: Set y2range in quals2.png plot
Petr Danecek [Wed, 18 Jul 2012 12:06:57 +0000 (13:06 +0100)]
Fix in output of missing haploid genotypes
Petr Danecek [Thu, 5 Jul 2012 17:30:12 +0000 (18:30 +0100)]
Allow filtering by read group or sample name in bamcheck. Bug fix in rm_info.
Petr Danecek [Thu, 5 Jul 2012 08:58:00 +0000 (09:58 +0100)]
VCF annotations with and without -m and more robust rm_info
Petr Danecek [Tue, 3 Jul 2012 12:03:26 +0000 (13:03 +0100)]
Bug fixes
Petr Danecek [Mon, 2 Jul 2012 10:36:41 +0000 (11:36 +0100)]
Alternative model for multiallelic and rare-variant calling. Proof-of-principle implementation.
Petr Danecek [Wed, 27 Jun 2012 05:33:29 +0000 (06:33 +0100)]
New -p switch for increased sensititivy of indel-calling. Here -m and -F are used per-sample which enables to detect rare indels in low-coverage bams. Experimental.
Petr Danecek [Thu, 21 Jun 2012 07:56:39 +0000 (08:56 +0100)]
Merge branch 'master' of github.com:samtools/samtools
Petr Danecek [Thu, 21 Jun 2012 07:56:13 +0000 (08:56 +0100)]
New -p option to start tview at desired position
Heng Li [Tue, 19 Jun 2012 17:06:23 +0000 (13:06 -0400)]
r579: after merging Peter's depad changes
Heng Li [Tue, 19 Jun 2012 16:45:47 +0000 (12:45 -0400)]
fixed a couple of minor compiling warnings
Heng Li [Tue, 19 Jun 2012 16:40:38 +0000 (09:40 -0700)]
Merge pull request #11 from peterjc/depad2
Depad2
peterjc [Tue, 19 Jun 2012 11:42:50 +0000 (12:42 +0100)]
Update @SQ lines during 'samtools depad'
Note does not (yet) preserve additional @SQ line tags (e.g. AS, SP, UR).
peterjc [Tue, 12 Jun 2012 14:33:03 +0000 (15:33 +0100)]
Calculate unpadded reference length, update BAM header (SAM header pending)
peterjc [Tue, 12 Jun 2012 14:29:26 +0000 (15:29 +0100)]
SAM/BAM input to 'samtools depad' not linked to FASTA reference
peterjc [Mon, 14 May 2012 15:33:52 +0000 (16:33 +0100)]
Wording of error messages
peterjc [Wed, 4 Apr 2012 10:43:12 +0000 (11:43 +0100)]
Catch missing reference error in faidx (avoids floating point exception)
peterjc [Wed, 4 Apr 2012 09:54:16 +0000 (10:54 +0100)]
Check embedded reference against FASTA if given in 'samtools depad'
peterjc [Wed, 4 Apr 2012 09:53:35 +0000 (10:53 +0100)]
Use FASTA file when no embedded reference in 'samtools depad'
peterjc [Wed, 4 Apr 2012 08:41:49 +0000 (09:41 +0100)]
Load FAI in 'samtools depad' (not used yet)
peterjc [Tue, 3 Apr 2012 15:05:00 +0000 (16:05 +0100)]
Add reference FASTA file to 'samtools depad' command line (not used yet)
peterjc [Tue, 3 Apr 2012 14:23:36 +0000 (15:23 +0100)]
Support SAM or BAM input/output in 'samtools depad' (default still BAM -> BAM)
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