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git.donarmstrong.com Git - samtools.git/log
peterjc [Fri, 19 Apr 2013 15:54:14 +0000 (16:54 +0100)]
Should update POS on unmapped reads in 'samtools depad'
Previously unmapped reads with a POS entry (e.g. those reads with
a mate which was mapped) were not being updated.
This has passed my testing with some non-trivial de novo MIRA 3.9
assemblies, coupled with the new 'samtools index' BIN verification.
peterjc [Fri, 19 Apr 2013 14:18:49 +0000 (15:18 +0100)]
Update 'samtools depad' help text regarding FASTA reference file
peterjc [Fri, 19 Apr 2013 14:13:32 +0000 (15:13 +0100)]
Verify old BIN value of reads during 'samtools index'.
This simple check catches invalid BIN values in reads which can cause
subtle bugs due to position-based retrieval missing data, and simple
out of bounds errors if a BIN is used beyond the length of the reference.
peterjc [Fri, 19 Apr 2013 11:08:42 +0000 (12:08 +0100)]
Update BIN values in 'samtools depad'
By its nature, 'samtools depad' edits mapped reads, altering both
the mapping position and CIGAR string. This means the mapped start
and end can change, and therefore the BIN can change.
Prior to this fix the pre-editing BIN (from the padded reference)
was being written to the BAM output, leading to subtle problems
downstream when trying to use the depadded BAM file via the BAI
index. For example, in Picard v1.89 this could trigger an
java.lang.ArrayIndexOutOfBoundsException where an old BIN was
outside the length of the unpadded reference sequence.
Petr Danecek [Fri, 5 Apr 2013 14:31:19 +0000 (15:31 +0100)]
bgzip now compiles
Petr Danecek [Tue, 26 Mar 2013 10:47:06 +0000 (10:47 +0000)]
The indel stats (IS) annotation splitted into two: IDV and IMF
Petr Danecek [Wed, 20 Mar 2013 15:56:50 +0000 (15:56 +0000)]
mpileup indel hotfix: fix in detecting long stretches of N's. The version string can be now overriden, either directly or using git-stamp Makefile rule
Petr Danecek [Wed, 20 Mar 2013 14:09:08 +0000 (14:09 +0000)]
mpileup fix: Print error message and exit when no files given. (On behalf of Gert Hulselmans)
Petr Danecek [Mon, 18 Mar 2013 14:43:36 +0000 (14:43 +0000)]
bcftools: version bump
Petr Danecek [Fri, 15 Mar 2013 11:49:21 +0000 (11:49 +0000)]
Version bump
Petr Danecek [Fri, 15 Mar 2013 10:12:23 +0000 (10:12 +0000)]
Updated NEWS document
Petr Danecek [Fri, 15 Mar 2013 09:27:09 +0000 (09:27 +0000)]
Merge remote branch 'pd3master/master'
Petr Danecek [Fri, 15 Mar 2013 09:25:33 +0000 (10:25 +0100)]
Get rid of %ld-with-int64_t warning on Mac
Petr Danecek [Fri, 15 Mar 2013 09:15:51 +0000 (09:15 +0000)]
Updated man pages
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 13:33:25 +0000 (13:33 +0000)]
Fixed brackets missing in the previous commit
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