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git.donarmstrong.com Git - samtools.git/log
Heng Li [Thu, 16 Sep 2010 17:38:43 +0000 (17:38 +0000)]
* added varFilter to vcfutils.pl
* reimplement realn(). now it performs a local alignment
* added cap_mapQ() to cap mapping quality when there are many substitutions
Heng Li [Wed, 15 Sep 2010 04:18:31 +0000 (04:18 +0000)]
* convert BCF to QCALL input
Heng Li [Wed, 15 Sep 2010 02:41:50 +0000 (02:41 +0000)]
dynamic band width in realignment
Heng Li [Wed, 15 Sep 2010 02:05:32 +0000 (02:05 +0000)]
fixed a bug in realignment
Heng Li [Wed, 15 Sep 2010 00:54:09 +0000 (00:54 +0000)]
fixed a minor issue
Heng Li [Tue, 14 Sep 2010 23:25:10 +0000 (23:25 +0000)]
fixed a bug in realignment
Heng Li [Tue, 14 Sep 2010 23:18:24 +0000 (23:18 +0000)]
minor changes. It is BUGGY now!
Heng Li [Tue, 14 Sep 2010 20:32:33 +0000 (20:32 +0000)]
* aggressive gapped aligner is implemented in calmd.
* distinguish gap_open and gap_end_open in banded alignment
* make tview accepts alignment with heading and tailing D
On behalf of John Marshall [Tue, 14 Sep 2010 13:04:28 +0000 (13:04 +0000)]
Add svn:ignore properties for generated files that don't appear in "make all".
On behalf of John Marshall [Mon, 13 Sep 2010 12:37:53 +0000 (12:37 +0000)]
Add svn:ignore properties listing the generated files.
(Except for *.o, which we'll assume is in global-ignores.)
Heng Li [Wed, 8 Sep 2010 16:53:55 +0000 (16:53 +0000)]
* samtools-0.1.8-13 (r715)
* fixed a bug in identifying SM across files
* bcftools: estimate heterozygosity
* bcftools: allow to skip sites without reference bases
Heng Li [Fri, 3 Sep 2010 21:19:12 +0000 (21:19 +0000)]
quite a lot changes to the contrast caller, but I still feel something is missing...
Heng Li [Fri, 3 Sep 2010 04:30:48 +0000 (04:30 +0000)]
* changed 3.434 to 4.343 (typo!)
* fixed a bug in the contrast caller
* calculate heterozygosity
Heng Li [Thu, 2 Sep 2010 03:24:47 +0000 (03:24 +0000)]
SNP calling from the GL field
Heng Li [Wed, 1 Sep 2010 22:52:30 +0000 (22:52 +0000)]
fixed another problem
Heng Li [Wed, 1 Sep 2010 22:31:17 +0000 (22:31 +0000)]
* fixed bugs in parsing VCF
* parser now works with GT/GQ/DP/PL/GL
Heng Li [Wed, 1 Sep 2010 19:28:29 +0000 (19:28 +0000)]
Do not compile _BCF_QUAD by default
Heng Li [Wed, 1 Sep 2010 19:21:41 +0000 (19:21 +0000)]
Write the correct ALT and PL in the SNP calling mode.
Heng Li [Wed, 1 Sep 2010 16:50:33 +0000 (16:50 +0000)]
more commands for my own uses
Heng Li [Wed, 1 Sep 2010 13:26:10 +0000 (13:26 +0000)]
Utilities for processing VCF
Heng Li [Tue, 31 Aug 2010 20:44:57 +0000 (20:44 +0000)]
preliminary contrast variant caller
Heng Li [Tue, 31 Aug 2010 16:28:39 +0000 (16:28 +0000)]
z' and z'' can be calculated
Heng Li [Tue, 31 Aug 2010 14:20:57 +0000 (14:20 +0000)]
* rename vcfout.c as call1.c
* prepare to add two-sample comparison
Heng Li [Tue, 24 Aug 2010 19:28:16 +0000 (19:28 +0000)]
fixed a bug in calculating the t statistics
Heng Li [Tue, 24 Aug 2010 18:05:50 +0000 (18:05 +0000)]
* samtools-0.1.8-13 (r698)
* perform one-tailed t-test for baseQ, mapQ and endDist
Heng Li [Tue, 24 Aug 2010 16:30:13 +0000 (16:30 +0000)]
added regularized incomplete beta function
Heng Li [Mon, 23 Aug 2010 21:36:17 +0000 (21:36 +0000)]
change the default correlation coefficient
Heng Li [Mon, 23 Aug 2010 18:46:52 +0000 (18:46 +0000)]
print QUAL as floating numbers
Heng Li [Mon, 23 Aug 2010 18:06:07 +0000 (18:06 +0000)]
* samtools-0.1.8-12 (r692)
* group data by samples in "mpileup -g"
Heng Li [Mon, 23 Aug 2010 14:58:53 +0000 (14:58 +0000)]
remove VCF output in mpileup
Heng Li [Mon, 23 Aug 2010 14:48:20 +0000 (14:48 +0000)]
* use the revised MAQ error model for mpileup
* prepare to remove the independent model from mpileup
Heng Li [Fri, 20 Aug 2010 19:46:40 +0000 (19:46 +0000)]
added revised MAQ error model
Heng Li [Wed, 18 Aug 2010 13:55:20 +0000 (13:55 +0000)]
allow to read the prior from the error output. EM iteration is working.
Heng Li [Tue, 17 Aug 2010 16:12:20 +0000 (16:12 +0000)]
* write a little more VCF header
* concatenate BCFs
Heng Li [Tue, 17 Aug 2010 00:53:16 +0000 (00:53 +0000)]
use float for QUAL
Heng Li [Sat, 14 Aug 2010 04:11:13 +0000 (04:11 +0000)]
faster for large sample size (in principle)
Heng Li [Sat, 14 Aug 2010 03:28:31 +0000 (03:28 +0000)]
* a numerically stable method to calculate z_{jk}
* currently slower than the old method but will be important for large sample size
* in principle, we can speed up for large n, but have not tried
Heng Li [Thu, 12 Aug 2010 01:58:31 +0000 (01:58 +0000)]
fixed an issue in parsing integer
Heng Li [Mon, 9 Aug 2010 17:05:07 +0000 (17:05 +0000)]
do not print refname if file is converted from VCF
Heng Li [Mon, 9 Aug 2010 16:59:47 +0000 (16:59 +0000)]
* parse PL
* fixed a bug in parsing VCF
Heng Li [Mon, 9 Aug 2010 16:49:23 +0000 (16:49 +0000)]
* fixed a bug in kstrtok@kstring.c
* preliminary VCF parser (not parse everything for now)
* improved view interface
Heng Li [Mon, 9 Aug 2010 14:43:13 +0000 (14:43 +0000)]
* improved kstring (added kstrtok)
* removed the limit on the format string length in bcftools
* use kstrtok to parse format which fixed a bug in the old code
Heng Li [Mon, 9 Aug 2010 05:12:05 +0000 (05:12 +0000)]
help messages
Heng Li [Mon, 9 Aug 2010 04:01:52 +0000 (04:01 +0000)]
perform single-tail test for ED4
Heng Li [Mon, 9 Aug 2010 03:48:35 +0000 (03:48 +0000)]
* test depth, end distance and HWE
Heng Li [Sun, 8 Aug 2010 06:04:15 +0000 (06:04 +0000)]
reimplement incomplete gamma functions. no copy-paste
Heng Li [Sat, 7 Aug 2010 02:42:54 +0000 (02:42 +0000)]
* bcftools: add HWE (no testing for now)
* record end dist in a 2x2 table, not avg, std any more
Heng Li [Fri, 6 Aug 2010 21:30:16 +0000 (21:30 +0000)]
* Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
* Not using Numerical Recipe due to licensing issues
Heng Li [Fri, 6 Aug 2010 03:46:53 +0000 (03:46 +0000)]
Fisher's exact test
Heng Li [Fri, 6 Aug 2010 01:48:33 +0000 (01:48 +0000)]
* samtools-0.1.8-11 (r672)
* collect more stats for allele balance test in bcftools (not yet)
Heng Li [Thu, 5 Aug 2010 20:17:58 +0000 (20:17 +0000)]
* the code base is stablized again.
* I will delay the vcf parser, which is quite complicated but with little value for now
Heng Li [Thu, 5 Aug 2010 20:03:23 +0000 (20:03 +0000)]
minor
Heng Li [Thu, 5 Aug 2010 20:03:08 +0000 (20:03 +0000)]
unfinished vcf parser
Heng Li [Thu, 5 Aug 2010 19:46:40 +0000 (19:46 +0000)]
* added prelimiary VCF parser (not finished)
* change struct a bit
Heng Li [Wed, 4 Aug 2010 02:35:27 +0000 (02:35 +0000)]
* allow to set min base q
* fixed a bug in mpileup -u
Heng Li [Wed, 4 Aug 2010 02:08:44 +0000 (02:08 +0000)]
spec
Heng Li [Wed, 4 Aug 2010 01:18:57 +0000 (01:18 +0000)]
added more examples
Heng Li [Wed, 4 Aug 2010 01:13:00 +0000 (01:13 +0000)]
fixed compilation error
Heng Li [Wed, 4 Aug 2010 01:04:00 +0000 (01:04 +0000)]
move bcftools to samtools
Heng Li [Tue, 3 Aug 2010 19:58:32 +0000 (19:58 +0000)]
fixed another minor bug
Heng Li [Tue, 3 Aug 2010 19:06:45 +0000 (19:06 +0000)]
* samtools-0.1.8-10 (r658)
* fixed a bug in bam2bcf when the reference is N
Heng Li [Tue, 3 Aug 2010 18:50:23 +0000 (18:50 +0000)]
* fixed a bug
* treat ambiguous ref base as the fifth base
Heng Li [Mon, 2 Aug 2010 21:38:27 +0000 (21:38 +0000)]
missing a column in VCF output...
Heng Li [Mon, 2 Aug 2010 21:31:33 +0000 (21:31 +0000)]
fixed a memory leak
Heng Li [Mon, 2 Aug 2010 21:27:31 +0000 (21:27 +0000)]
fixed a bug in bcf reader
Heng Li [Mon, 2 Aug 2010 21:00:41 +0000 (21:00 +0000)]
fixed a bug
Heng Li [Mon, 2 Aug 2010 20:49:35 +0000 (20:49 +0000)]
* samtools-0.1.8-9 (r649)
* lossless representation of PL in BCF output
Heng Li [Mon, 2 Aug 2010 20:07:25 +0000 (20:07 +0000)]
Generate binary VCF
Heng Li [Wed, 28 Jul 2010 15:59:19 +0000 (15:59 +0000)]
* samtools-0.1.8-8 (r644)
* mpileup becomes a little stable again
* the method is slightly different, but is more theoretically correct
* snp calling is O(n^2) instead of O(n^3)
Heng Li [Wed, 28 Jul 2010 15:54:15 +0000 (15:54 +0000)]
* fixed a STUPID bug, which cost me a lot of time.
* I am going to clean up mcns a little bit
Heng Li [Wed, 28 Jul 2010 03:23:07 +0000 (03:23 +0000)]
supposedly this is THE correct implementation, but more testing is needed
Heng Li [Wed, 28 Jul 2010 02:43:39 +0000 (02:43 +0000)]
NOT ready yet. Going to make further changes...
Heng Li [Mon, 26 Jul 2010 02:18:38 +0000 (02:18 +0000)]
* samtools-0.1.8-7 (r639)
* fixed the reference allele assignment
Heng Li [Sun, 25 Jul 2010 16:01:26 +0000 (16:01 +0000)]
* samtools-0.1.8-6 (r638)
* skip isnan/isinf in case of float underflow
* added the flat prior
* fixed an issue where there are no reads supporting the reference
Heng Li [Sat, 24 Jul 2010 18:16:27 +0000 (18:16 +0000)]
minor changes
Heng Li [Sat, 24 Jul 2010 18:07:27 +0000 (18:07 +0000)]
minor tweaks
Heng Li [Sat, 24 Jul 2010 05:49:49 +0000 (05:49 +0000)]
posterior expectation FINALLY working. I am so tired...
Heng Li [Fri, 23 Jul 2010 17:50:48 +0000 (17:50 +0000)]
another minor fix to mpileup
Heng Li [Fri, 23 Jul 2010 17:43:31 +0000 (17:43 +0000)]
added the format column
Heng Li [Fri, 23 Jul 2010 17:25:44 +0000 (17:25 +0000)]
added an alternative prior
Heng Li [Fri, 23 Jul 2010 15:48:51 +0000 (15:48 +0000)]
calculate posterior allele frequency
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.
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
Heng Li [Wed, 14 Jul 2010 20:26:27 +0000 (20:26 +0000)]
* samtools-0.1.8-2 (r617)
* allele frequency calculation apparently works...
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
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
Heng Li [Mon, 12 Jul 2010 02:40:56 +0000 (02:40 +0000)]
Release samtools-0.1.8
Heng Li [Mon, 12 Jul 2010 01:08:56 +0000 (01:08 +0000)]
fixed a compiling issue for Windows
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)
Heng Li [Fri, 9 Jul 2010 21:05:10 +0000 (21:05 +0000)]
change the command line option of pileup
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
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
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.
Heng Li [Thu, 8 Jul 2010 05:05:19 +0000 (05:05 +0000)]
removed a debugging example
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).
Heng Li [Fri, 2 Jul 2010 23:32:24 +0000 (23:32 +0000)]
fixed a minor bug in idxstats
Heng Li [Wed, 16 Jun 2010 13:03:59 +0000 (13:03 +0000)]
fixed a minor bug in indexing
Heng Li [Tue, 15 Jun 2010 14:17:53 +0000 (14:17 +0000)]
change printf() to puts in exporting
Heng Li [Mon, 14 Jun 2010 01:41:11 +0000 (01:41 +0000)]
minor fix. No actual effect.
Heng Li [Mon, 14 Jun 2010 01:32:45 +0000 (01:32 +0000)]
added Makefile targets to compile shared/dynamic library