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samtools.git
2012-03-18
Heng Li
bugfix in caching
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2012-03-18
Heng Li
multi-threading working on toy examples
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2012-03-18
Heng Li
preliminary implementation; not tested
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2012-03-18
Heng Li
updated with the latest bgzf library
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2012-03-09
Heng Li
On behalf of Petr: multi-allelic GT
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2012-03-09
Heng Li
Removed SVN ChangeLog; merged my private github Log...
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2012-03-09
Heng Li
doc for downsampling
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2012-03-09
Heng Li
another example, used by g1k for QA
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2012-03-09
Heng Li
Two auxilary Lua scripts
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2012-03-09
Heng Li
Incoporated changes from Nils Homer.
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2012-02-16
Heng Li
bugfix: wrong SP; missing DV in the VCF header
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2012-02-08
Heng Li
changes from git
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2011-09-28
Heng Li
unpadded output
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2011-09-23
Heng Li
added the ace2sam converter
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2011-09-23
Heng Li
converted padded SAM to unpadded SAM
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2011-09-02
Heng Li
* Updated samtools to the latest
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2011-08-17
Heng Li
* bugfix in index: large memory when a read pos is 1
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2011-07-15
Heng Li
allow to set seed in view-subsampling
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2011-07-15
Heng Li
subsampling read pairs
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2011-07-13
Heng Li
support trio indels
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2011-07-07
Heng Li
for WIN32 compatibility
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2011-07-07
Heng Li
fixed a bug in bam_plcmd.c
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2011-07-07
Heng Li
Release samtools-0.1.17
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2011-06-15
Heng Li
fixed a bug caused by a recent patch
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2011-06-03
Heng Li
* 0.1.16-dev (r969:252)
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2011-04-22
Heng Li
Removed the pileup command
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2011-04-22
Heng Li
Release samtools-0.1.16 (r963:234)
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2011-04-21
Heng Li
fixed a bug in merge
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2011-04-18
Heng Li
Added the support for the new SAM/BAM type "B"
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2011-04-17
Heng Li
* fixed a bug in bedidx: input BED not sorted
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2011-04-15
Heng Li
* Added Brent's method for frequency estimate
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2011-04-10
Heng Li
Release samtools-0.1.15 (r949:203)
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2011-04-08
Heng Li
* added bam_verbose global variable
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2011-04-01
Heng Li
added quality filtering
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2011-04-01
Heng Li
fixed a few typos in comments
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2011-04-01
Heng Li
Added an example of using mpileup
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2011-03-31
Heng Li
* synchronize bgzf in tabix and in samtools
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2011-03-30
Heng Li
* added BED support to samtools view and mpileup and...
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2011-03-22
Heng Li
Release samtools-0.1.14 (r933:170)
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2011-03-18
Heng Li
forget to add this file
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2011-03-18
Heng Li
* allow to change the compression level in BAM output
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2011-03-18
Heng Li
export2sam.pl-2.3.1, provided by Chris Saunders from...
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2011-03-08
Heng Li
added the haploid mode
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2011-03-01
Heng Li
Release samtools-0.1.13 (r926:134)
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2011-03-01
Heng Li
* optionally drop phase ambiguous reads
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2011-02-28
Heng Li
minor changes to a heuristic rule
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2011-02-28
Heng Li
* 0.1.12-r924:126
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2011-02-28
Heng Li
* put version number in bam.h
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2011-02-25
Heng Li
* change the order of PL/GL according to the latest...
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2011-02-25
Heng Li
update the BCF spec
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2011-02-25
Heng Li
added the phase command
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2011-02-24
Heng Li
added "const" to bcf_p1_cal()
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2011-02-24
Heng Li
more meaningful BAM truncation message
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2011-02-24
Heng Li
* automatically fix errors in GL
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2011-02-11
Heng Li
finished VCF->BCF conversion
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2011-02-03
Petr Danecek
Prevent division by zero
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2011-02-02
Heng Li
fixed a typo in the VCF header
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2011-02-02
Heng Li
* fixed an out-of-boundary bug
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2011-01-30
Heng Li
* avoid a segfault when network connect fails
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2011-01-27
Heng Li
* fixed a rare memory issue in bam_md.c
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2011-01-24
Heng Li
fixed two minor bugs in Fisher's exact test
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2011-01-19
Petr Danecek
Skip sites with unknown ref
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2011-01-15
Heng Li
move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
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2011-01-06
Heng Li
* samtools-0.1.12-10 (r896)
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2011-01-04
Heng Li
sorry. It is SP not ST
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2011-01-04
Heng Li
added ST
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2011-01-04
Petr Danecek
Fixed a typo in read_samples
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2010-12-28
On behalf of...
System libraries go *after* user libraries in link...
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2010-12-21
Heng Li
* samtools-0.1.12-9 (r891)
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2010-12-15
Heng Li
* samtools-0.1.12-12 (r889)
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2010-12-15
Heng Li
When -B is applied to mpileup, still use paired reads...
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2010-12-15
Heng Li
* samtools-0.1.12-6 (r887)
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2010-12-14
Heng Li
(Arguably) improved the indel caller a tiny bit for...
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2010-12-14
Petr Danecek
Fixed the VCF header to pass validation
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2010-12-13
Heng Li
* samtools-0.1.12-4 (r884)
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2010-12-12
Heng Li
compute max SP and max GQ from sample genotypes
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2010-12-10
Heng Li
drop bcf-fix.pl as it is redundant by the latest changes
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2010-12-10
Heng Li
* fixed a minor issue in printing VCFs
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2010-12-10
Heng Li
Make sure that the GT genotype field is the first
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2010-12-08
Heng Li
* samtools-0.1.12-2 (r877)
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2010-12-08
Heng Li
a spelling error..
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2010-12-08
Heng Li
* samtools-0.1.12-1 (r873)
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2010-12-07
Heng Li
fixed a bug in vcf2fq
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2010-12-05
Heng Li
added a warning for the Windows version
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2010-12-05
Heng Li
In ksprintf(), change "%lf" and "%lg" to "%f" and ...
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2010-12-05
Heng Li
bring back the windows support
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2010-12-05
Heng Li
Fixed a compiling error when knetfile is not used.
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2010-12-04
Heng Li
vcf->fastq
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2010-12-03
Heng Li
* remove "-f". Instead always compute consensus quality
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2010-12-03
Heng Li
more informative error message
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2010-12-02
Heng Li
Release samtools-0.1.12a
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2010-12-02
Heng Li
a possible fix to DP4=0,0,0,0; have not tested, but...
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2010-12-02
Heng Li
Release samtools-0.1.12
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2010-12-02
Heng Li
* samtools-0.1.11-1 (r858)
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2010-12-01
Heng Li
fixed a memory leak in bam_fetch()
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2010-11-26
Heng Li
* fixed a memory violation
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2010-11-23
Heng Li
fixed a typo/bug in r^2 computation
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2010-11-22
Heng Li
forget to change the version information
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2010-11-22
Heng Li
Release samtools-0.1.11
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2010-11-20
Heng Li
* samtools-0.1.10-9 (r844)
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