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samtools.git
2012-05-17
Heng Li
added bamshuf from htslib
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2012-05-11
Heng Li
bugfix: bgzf-mt may write prematured output
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2012-05-05
Heng Li
added length threshold
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2012-05-03
Petr Danecek
Reverted to the previous behaviour, the unmapped reads...
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2012-04-24
Petr Danecek
init_regions: check for non-matching sequence names
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2012-04-23
Petr Danecek
Resolved merge conflict
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2012-04-23
Petr Danecek
Indexed access can be now combined with target regions...
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2012-04-17
Heng Li
r572: added "bedcov" command
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2012-04-17
Heng Li
change getline() to mygetline()
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2012-04-17
Heng Li
updated to the latest kseq
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2012-04-12
Petr Danecek
Added check for out-of-bounds indels at the end of...
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2012-04-12
Petr Danecek
On behalf of Bradford Powell: fixed typo in VCF header...
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2012-04-04
Petr Danecek
Removed glibc dependency (getline)
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2012-04-04
Petr Danecek
Merge remote branch 'main/master'
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2012-04-03
Heng Li
Merge branch 'master' of github.com:samtools/samtools
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2012-04-03
Heng Li
compiling errors on some machines
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2012-04-02
Petr Danecek
Temporary fix to prevent segfault in kpa_glocal
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2012-03-30
Heng Li
shrink bam1_t::m_data when sorting
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2012-03-29
Heng Li
Merge branch 'master' of github.com:samtools/samtools...
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2012-03-29
samtools
Merge pull request #2 from peterjc/depad
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2012-03-29
Petr Danecek
Compile cleanly from top-level Makefile. Check for...
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2012-03-29
Petr Danecek
Compile cleanly from top-level Makefile. Check for...
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2012-03-28
Petr Danecek
Added rule for bamcheck creation
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2012-03-28
Petr Danecek
Added rule for bamcheck creation
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2012-03-27
Petr Danecek
Initial release of bamcheck and plot-bamcheck
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2012-03-27
Petr Danecek
Initial release of bamcheck and plot-bamcheck
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2012-03-26
peterjc
Check reference length in BAM header against embedded...
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2012-03-26
peterjc
Cope with trailing CIGAR H (or S and H) in 'samtools...
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2012-03-26
peterjc
Cope with leading CIGAR H (or H and S) in 'samtools...
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2012-03-26
peterjc
Tolerate CIGAR H operators in 'samtools depad'
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2012-03-26
peterjc
Include leading CIGAR P operators in 'samtools depad'
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2012-03-26
peterjc
Record actual sequence in unpad_seq (fixes apparently...
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2012-03-24
Heng Li
filter on query sequence length (not aln len)
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2012-03-24
Heng Li
move seqtk to a separate project
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2012-03-23
peterjc
Correct my error message; assed some comments
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2012-03-23
peterjc
Add TODO note about reference lengths
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2012-03-23
peterjc
Cope with CIGAR D or P to mark gaps in an embedded...
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2012-03-22
peterjc
Check current reference sequence matches RNAME in samto...
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2012-03-22
peterjc
Support CIGAR X/= in depad
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2012-03-22
peterjc
Helpful error message on bad CIGAR in unpad_seq
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2012-03-22
Heng Li
change SO
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2012-03-22
Heng Li
a little more accurate mem estimate
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2012-03-22
Heng Li
control compression level at command line
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2012-03-20
Heng Li
optionally surpress /[12] in bam2fq
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2012-03-20
Heng Li
Merge branch 'master' into mt
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2012-03-20
Heng Li
bugfix: downsampling not always working
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2012-03-19
Heng Li
name sorting checkes READ1 and READ2
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2012-03-19
Heng Li
sorting also considers strand
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2012-03-18
Heng Li
change the default block size in sorting
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2012-03-18
Heng Li
multi-threaded sorting
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2012-03-18
Heng Li
added .gitignore
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2012-03-18
Heng Li
added mt comression to merge
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2012-03-18
Heng Li
updated the alphanum comparison function
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2012-03-18
Heng Li
avoid wasting CPU time by the master thread
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2012-03-18
Heng Li
use conditional variable
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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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