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git.donarmstrong.com Git - samtools.git/log
Heng Li [Fri, 1 Apr 2011 03:17:03 +0000 (03:17 +0000)]
Added an example of using mpileup
Heng Li [Thu, 31 Mar 2011 20:38:57 +0000 (20:38 +0000)]
* synchronize bgzf in tabix and in samtools
* fixed a severe bug in bedidx.c
Heng Li [Wed, 30 Mar 2011 18:35:53 +0000 (18:35 +0000)]
* added BED support to samtools view and mpileup and bcftools view
* ML estimate of allele frequency in two groups
* better error message given inconsisten RG labels
* compute all-pair r^2
Heng Li [Tue, 22 Mar 2011 03:08:31 +0000 (03:08 +0000)]
Release samtools-0.1.14 (r933:170)
Heng Li [Fri, 18 Mar 2011 20:34:14 +0000 (20:34 +0000)]
forget to add this file
Heng Li [Fri, 18 Mar 2011 20:33:51 +0000 (20:33 +0000)]
* allow to change the compression level in BAM output
* use compress level 1 in sorting
* association test
* concatenate BAMs
* allow to threshold on max depth in INDEL calling
Heng Li [Fri, 18 Mar 2011 19:23:06 +0000 (19:23 +0000)]
export2sam.pl-2.3.1, provided by Chris Saunders from Illumina Inc.
Heng Li [Tue, 8 Mar 2011 03:07:35 +0000 (03:07 +0000)]
added the haploid mode
Heng Li [Tue, 1 Mar 2011 19:48:25 +0000 (19:48 +0000)]
Release samtools-0.1.13 (r926:134)
Heng Li [Tue, 1 Mar 2011 14:51:01 +0000 (14:51 +0000)]
* optionally drop phase ambiguous reads
* write vcf format 4.1 instead of 4.0
Heng Li [Mon, 28 Feb 2011 20:45:17 +0000 (20:45 +0000)]
minor changes to a heuristic rule
Heng Li [Mon, 28 Feb 2011 20:24:04 +0000 (20:24 +0000)]
* 0.1.12-r924:126
* fixed a bug in phase (due to recent changes)
* fixed a bug in vcf2fq
Heng Li [Mon, 28 Feb 2011 17:57:39 +0000 (17:57 +0000)]
* put version number in bam.h
* write version to BCF
* in phase, change the default -q to 37
* output a little more information during phasing
Heng Li [Fri, 25 Feb 2011 21:40:09 +0000 (21:40 +0000)]
* change the order of PL/GL according to the latest VCF spec
* change the type of SP to int32_t
Heng Li [Fri, 25 Feb 2011 19:40:56 +0000 (19:40 +0000)]
update the BCF spec
Heng Li [Fri, 25 Feb 2011 05:59:27 +0000 (05:59 +0000)]
added the phase command
Heng Li [Thu, 24 Feb 2011 15:05:54 +0000 (15:05 +0000)]
added "const" to bcf_p1_cal()
Heng Li [Thu, 24 Feb 2011 14:36:30 +0000 (14:36 +0000)]
more meaningful BAM truncation message
Heng Li [Thu, 24 Feb 2011 14:35:06 +0000 (14:35 +0000)]
* automatically fix errors in GL
* output unrecognized FORMAT as "."
Heng Li [Fri, 11 Feb 2011 03:59:47 +0000 (03:59 +0000)]
finished VCF->BCF conversion
Petr Danecek [Thu, 3 Feb 2011 08:13:48 +0000 (08:13 +0000)]
Prevent division by zero
Heng Li [Wed, 2 Feb 2011 16:29:20 +0000 (16:29 +0000)]
fixed a typo in the VCF header
Heng Li [Wed, 2 Feb 2011 16:28:24 +0000 (16:28 +0000)]
* fixed an out-of-boundary bug
* improved sorting order checking in index
Heng Li [Sun, 30 Jan 2011 03:59:20 +0000 (03:59 +0000)]
* avoid a segfault when network connect fails
* update INSTALL
* fixed a bug in tview on big-endian by Nathan Weeks
Heng Li [Thu, 27 Jan 2011 19:50:02 +0000 (19:50 +0000)]
* fixed a rare memory issue in bam_md.c
* fixed a bug in indel calling related to unmapped and refskip reads
Heng Li [Mon, 24 Jan 2011 02:46:18 +0000 (02:46 +0000)]
fixed two minor bugs in Fisher's exact test
Petr Danecek [Wed, 19 Jan 2011 14:28:02 +0000 (14:28 +0000)]
Skip sites with unknown ref
Heng Li [Sat, 15 Jan 2011 17:56:05 +0000 (17:56 +0000)]
move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
Heng Li [Thu, 6 Jan 2011 15:52:15 +0000 (15:52 +0000)]
* samtools-0.1.12-10 (r896)
* allow to exclude read groups in mpileup
Heng Li [Tue, 4 Jan 2011 16:31:29 +0000 (16:31 +0000)]
sorry. It is SP not ST
Heng Li [Tue, 4 Jan 2011 16:29:06 +0000 (16:29 +0000)]
added ST
Petr Danecek [Tue, 4 Jan 2011 11:55:56 +0000 (11:55 +0000)]
Fixed a typo in read_samples
On behalf of John Marshall [Tue, 28 Dec 2010 13:06:49 +0000 (13:06 +0000)]
System libraries go *after* user libraries in link commands, because
the user libraries may themselves have dependencies that are satisfied
by the system libraries. It's not rocket science!
This makes a difference with some linkers; or with -static or --as-needed.
The examples/Makefile fix is from Charles Plessy.
See also http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606004
Heng Li [Tue, 21 Dec 2010 17:16:33 +0000 (17:16 +0000)]
* samtools-0.1.12-9 (r891)
* allow to call SNPs from a subset of samples
Heng Li [Wed, 15 Dec 2010 16:28:16 +0000 (16:28 +0000)]
* samtools-0.1.12-12 (r889)
* set mapQ as 20 if it equals 255
Heng Li [Wed, 15 Dec 2010 03:41:09 +0000 (03:41 +0000)]
When -B is applied to mpileup, still use paired reads only unless -A is flagged.
Heng Li [Wed, 15 Dec 2010 03:37:05 +0000 (03:37 +0000)]
* samtools-0.1.12-6 (r887)
* added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.
Heng Li [Tue, 14 Dec 2010 17:51:03 +0000 (17:51 +0000)]
(Arguably) improved the indel caller a tiny bit for lowCov data.
Petr Danecek [Tue, 14 Dec 2010 09:55:46 +0000 (09:55 +0000)]
Fixed the VCF header to pass validation
Heng Li [Mon, 13 Dec 2010 04:02:19 +0000 (04:02 +0000)]
* samtools-0.1.12-4 (r884)
* fixed a long-existing flaw in the INDEL calling model
Heng Li [Sun, 12 Dec 2010 01:05:42 +0000 (01:05 +0000)]
compute max SP and max GQ from sample genotypes
Heng Li [Fri, 10 Dec 2010 15:50:54 +0000 (15:50 +0000)]
drop bcf-fix.pl as it is redundant by the latest changes
Heng Li [Fri, 10 Dec 2010 15:50:29 +0000 (15:50 +0000)]
* fixed a minor issue in printing VCFs
* write bcftools specific INFO and FORMAT in the header
Heng Li [Fri, 10 Dec 2010 15:09:14 +0000 (15:09 +0000)]
Make sure that the GT genotype field is the first
Heng Li [Wed, 8 Dec 2010 22:27:05 +0000 (22:27 +0000)]
* samtools-0.1.12-2 (r877)
* allow to fine control the selection of indel candidates. The current
setting is okay for lowCov and highCov with ~100 samples, but it
skips too many indels for highCov with >250 samples.
Heng Li [Wed, 8 Dec 2010 03:40:35 +0000 (03:40 +0000)]
a spelling error..
Heng Li [Wed, 8 Dec 2010 03:39:57 +0000 (03:39 +0000)]
* samtools-0.1.12-1 (r873)
* added a switch to allow anomalous read pairs in calling
Heng Li [Tue, 7 Dec 2010 19:43:54 +0000 (19:43 +0000)]
fixed a bug in vcf2fq
Heng Li [Sun, 5 Dec 2010 06:18:06 +0000 (06:18 +0000)]
added a warning for the Windows version
Heng Li [Sun, 5 Dec 2010 06:05:51 +0000 (06:05 +0000)]
In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
According to the manual page, this change is valid. However, MinGW seems
to interpret "%lf" as "%Lf".
Heng Li [Sun, 5 Dec 2010 05:35:43 +0000 (05:35 +0000)]
bring back the windows support
Heng Li [Sun, 5 Dec 2010 04:33:51 +0000 (04:33 +0000)]
Fixed a compiling error when knetfile is not used.
Heng Li [Sat, 4 Dec 2010 05:13:22 +0000 (05:13 +0000)]
vcf->fastq
Heng Li [Fri, 3 Dec 2010 22:12:30 +0000 (22:12 +0000)]
* remove "-f". Instead always compute consensus quality
* increase the upper limit of quality
Heng Li [Fri, 3 Dec 2010 20:28:15 +0000 (20:28 +0000)]
more informative error message
Heng Li [Thu, 2 Dec 2010 21:16:08 +0000 (21:16 +0000)]
Release samtools-0.1.12a
Heng Li [Thu, 2 Dec 2010 20:55:06 +0000 (20:55 +0000)]
a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect
Heng Li [Thu, 2 Dec 2010 16:39:57 +0000 (16:39 +0000)]
Release samtools-0.1.12
Heng Li [Thu, 2 Dec 2010 16:24:41 +0000 (16:24 +0000)]
* samtools-0.1.11-1 (r858)
* fixed a bug in mpileup which causes segfaults
* bcftools: do not segfault when BCF contains errors
Heng Li [Wed, 1 Dec 2010 04:52:50 +0000 (04:52 +0000)]
fixed a memory leak in bam_fetch()
Heng Li [Fri, 26 Nov 2010 05:07:31 +0000 (05:07 +0000)]
* fixed a memory violation
* added splitchr to vcfutils.pl
Heng Li [Tue, 23 Nov 2010 14:05:08 +0000 (14:05 +0000)]
fixed a typo/bug in r^2 computation
Heng Li [Mon, 22 Nov 2010 03:20:20 +0000 (03:20 +0000)]
forget to change the version information
Heng Li [Mon, 22 Nov 2010 03:16:52 +0000 (03:16 +0000)]
Release samtools-0.1.11
Heng Li [Sat, 20 Nov 2010 04:16:08 +0000 (04:16 +0000)]
* samtools-0.1.10-9 (r844)
* added the "folded" or reference-free mode for variant calling
Heng Li [Sat, 20 Nov 2010 03:26:36 +0000 (03:26 +0000)]
In merging, if -R is specified, do not abort if the sequence dictionary is different.
On behalf of John Marshall [Sat, 20 Nov 2010 02:24:28 +0000 (02:24 +0000)]
When merging BAM headers, compare the list of target reference sequences
strictly (and fail/abort if there is a mismatch), but allow one list to be a
prefix of the other. (i.e., check that the lists are identical up until the
shorter runs out, and add the excess targets from the longer to the output.)
Heng Li [Fri, 19 Nov 2010 19:49:27 +0000 (19:49 +0000)]
* samtools-0.1.10 (r841)
* fixed a bug in pileup when the first CIGAR operation is D
* fixed a bug in view with range query
Heng Li [Fri, 19 Nov 2010 18:45:51 +0000 (18:45 +0000)]
* samtools-0.1.10-4 (r840)
* drop the MNP caller. It is slow while does not diliver too much
benefit. Possibly I will work on it in future given more time.
* there is a segfault in pileup
* someone has reported segfault from view/index/sort
Heng Li [Thu, 18 Nov 2010 22:30:11 +0000 (22:30 +0000)]
* samtools-0.1.10-6 (r839)
* call MNPs without realignment because it seems to me that it is not
worthwhile to significantly slow down SNP calling.
* the result looks quite different from the previous version. I have
work to do...
Heng Li [Thu, 18 Nov 2010 16:26:09 +0000 (16:26 +0000)]
Apply a patch by Rob Davis, which improves fault detection.
Heng Li [Thu, 18 Nov 2010 16:09:23 +0000 (16:09 +0000)]
* samtools-r836
* initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
Heng Li [Thu, 18 Nov 2010 05:25:13 +0000 (05:25 +0000)]
* modify the filtering rule: also filter SNPs around filtered indels
* added MNP filter
Heng Li [Thu, 18 Nov 2010 04:13:52 +0000 (04:13 +0000)]
* samtools-0.1.10-4 (r834)
* fixed a silly bug in printing MNP
* restrict to at most 1 alternative allele
Heng Li [Thu, 18 Nov 2010 02:58:58 +0000 (02:58 +0000)]
fixed a bug in printing MNPs
Heng Li [Thu, 18 Nov 2010 02:47:20 +0000 (02:47 +0000)]
minor change to how seqQ is applied
Heng Li [Thu, 18 Nov 2010 02:41:12 +0000 (02:41 +0000)]
* samtools-0.1.10 (r831)
* initial MNP caller
Heng Li [Wed, 17 Nov 2010 04:14:15 +0000 (04:14 +0000)]
Release samtools-0.1.10 (r829)
Heng Li [Wed, 17 Nov 2010 01:48:49 +0000 (01:48 +0000)]
update version information: samtools-0.1.9-20 (r828)
Heng Li [Tue, 16 Nov 2010 20:32:50 +0000 (20:32 +0000)]
bcftools: allow to skip indels
Heng Li [Tue, 16 Nov 2010 19:11:58 +0000 (19:11 +0000)]
remove ZQ if both BQ and ZQ are present
Heng Li [Tue, 16 Nov 2010 18:51:33 +0000 (18:51 +0000)]
* samtools-0.1.9-18 (r825)
* change the behaviour of calmd such that by default it does not change the base quality
Heng Li [Tue, 16 Nov 2010 04:31:53 +0000 (04:31 +0000)]
* samtools-0.1.9-17 (r824)
* added command line options to change the default parameters in indel calling
* update the manual
Heng Li [Mon, 15 Nov 2010 17:20:13 +0000 (17:20 +0000)]
* samtools-0.1.9-r823
* the BQ tag is now 64 shifted, not 33 shifted
Heng Li [Mon, 15 Nov 2010 05:30:18 +0000 (05:30 +0000)]
* samtools-0.1.9-16 (r822)
* keep the raw depth because in indel calling, DP4 may be way off the true depth
Heng Li [Sat, 13 Nov 2010 06:18:31 +0000 (06:18 +0000)]
* samtools-0.1.9-15 (r821)
* calmd: write BQ
* skip realignment if BQ is present
Heng Li [Sat, 13 Nov 2010 06:08:26 +0000 (06:08 +0000)]
* samtools-0.1.9-14 (r820)
* penalize reads with excessive differences in indel calling
Heng Li [Sat, 13 Nov 2010 02:36:27 +0000 (02:36 +0000)]
* samtools-0.1.9-13 (r819)
* fixed a bug in pileup given refskip
Heng Li [Fri, 12 Nov 2010 18:04:53 +0000 (18:04 +0000)]
* samtools-r818
* for indel calling, do two rounds of probabilistic realignments
Heng Li [Fri, 12 Nov 2010 01:04:07 +0000 (01:04 +0000)]
* samtools-0.1.19-11 (r817)
* only initiate indel calling when 0.2% of reads contain a gap
Heng Li [Thu, 11 Nov 2010 06:22:59 +0000 (06:22 +0000)]
* samtools-0.1.9-10 (r816)
* I know why the forward method fails. it is because of zero base
qualities. when that is fixed, the forward method seems to give
better results than Viterbi, as it should be. I am tired...
Heng Li [Thu, 11 Nov 2010 05:57:15 +0000 (05:57 +0000)]
effectively revert to the viterbi version. The forward realignment gives too many false positives.
Heng Li [Thu, 11 Nov 2010 05:18:02 +0000 (05:18 +0000)]
* samtools-0.1.9-9 (r810)
* use forward, instead of viterbi, for realignment
* realignment is now quality aware
Heng Li [Thu, 11 Nov 2010 03:45:24 +0000 (03:45 +0000)]
* prepare to replace kaln with kprobaln in realignment
Heng Li [Wed, 10 Nov 2010 22:28:50 +0000 (22:28 +0000)]
fixed a typo
Heng Li [Wed, 10 Nov 2010 21:54:46 +0000 (21:54 +0000)]
use zlib for direct reading when BCF_LITE is in use
Heng Li [Wed, 10 Nov 2010 21:32:13 +0000 (21:32 +0000)]
* do not use reads containing too many mismatches for indel calling
* fixed a trivial bug in case of multi-allelic indels
Heng Li [Wed, 10 Nov 2010 18:23:02 +0000 (18:23 +0000)]
* samtools-0.1.9-8 (r809)
* fixed a bug in the indel caller
Heng Li [Wed, 10 Nov 2010 17:24:10 +0000 (17:24 +0000)]
minor change to makefile
Heng Li [Wed, 10 Nov 2010 17:10:21 +0000 (17:10 +0000)]
* samtools-0.1.9-8 (r807)
* collect indel candidates only from specified platforms (@RG-PL)
* merge varFilter and filter4vcf in vcfutils.pl