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samtools.git
2012-05-17 Heng Liadded bamshuf from htslib commit | commitdiff | tree | snapshot
2012-05-11 Heng Libugfix: bgzf-mt may write prematured output commit | commitdiff | tree | snapshot
2012-05-05 Heng Liadded length threshold commit | commitdiff | tree | snapshot
2012-05-03 Petr DanecekReverted to the previous behaviour, the unmapped reads... commit | commitdiff | tree | snapshot
2012-04-24 Petr Danecekinit_regions: check for non-matching sequence names commit | commitdiff | tree | snapshot
2012-04-23 Petr DanecekResolved merge conflict commit | commitdiff | tree | snapshot
2012-04-23 Petr DanecekIndexed access can be now combined with target regions... commit | commitdiff | tree | snapshot
2012-04-17 Heng Lir572: added "bedcov" command commit | commitdiff | tree | snapshot
2012-04-17 Heng Lichange getline() to mygetline() commit | commitdiff | tree | snapshot
2012-04-17 Heng Liupdated to the latest kseq commit | commitdiff | tree | snapshot
2012-04-12 Petr DanecekAdded check for out-of-bounds indels at the end of... commit | commitdiff | tree | snapshot
2012-04-12 Petr DanecekOn behalf of Bradford Powell: fixed typo in VCF header... commit | commitdiff | tree | snapshot
2012-04-04 Petr DanecekRemoved glibc dependency (getline) commit | commitdiff | tree | snapshot
2012-04-04 Petr DanecekMerge remote branch 'main/master' commit | commitdiff | tree | snapshot
2012-04-03 Heng LiMerge branch 'master' of github.com:samtools/samtools commit | commitdiff | tree | snapshot
2012-04-03 Heng Licompiling errors on some machines commit | commitdiff | tree | snapshot
2012-04-02 Petr DanecekTemporary fix to prevent segfault in kpa_glocal commit | commitdiff | tree | snapshot
2012-03-30 Heng Lishrink bam1_t::m_data when sorting commit | commitdiff | tree | snapshot
2012-03-29 Heng LiMerge branch 'master' of github.com:samtools/samtools... commit | commitdiff | tree | snapshot
2012-03-29 samtoolsMerge pull request #2 from peterjc/depad commit | commitdiff | tree | snapshot
2012-03-29 Petr DanecekCompile cleanly from top-level Makefile. Check for... commit | commitdiff | tree | snapshot
2012-03-29 Petr DanecekCompile cleanly from top-level Makefile. Check for... commit | commitdiff | tree | snapshot
2012-03-28 Petr DanecekAdded rule for bamcheck creation commit | commitdiff | tree | snapshot
2012-03-28 Petr DanecekAdded rule for bamcheck creation commit | commitdiff | tree | snapshot
2012-03-27 Petr DanecekInitial release of bamcheck and plot-bamcheck commit | commitdiff | tree | snapshot
2012-03-27 Petr DanecekInitial release of bamcheck and plot-bamcheck commit | commitdiff | tree | snapshot
2012-03-26 peterjcCheck reference length in BAM header against embedded... commit | commitdiff | tree | snapshot
2012-03-26 peterjcCope with trailing CIGAR H (or S and H) in 'samtools... commit | commitdiff | tree | snapshot
2012-03-26 peterjcCope with leading CIGAR H (or H and S) in 'samtools... commit | commitdiff | tree | snapshot
2012-03-26 peterjcTolerate CIGAR H operators in 'samtools depad' commit | commitdiff | tree | snapshot
2012-03-26 peterjcInclude leading CIGAR P operators in 'samtools depad' commit | commitdiff | tree | snapshot
2012-03-26 peterjcRecord actual sequence in unpad_seq (fixes apparently... commit | commitdiff | tree | snapshot
2012-03-24 Heng Lifilter on query sequence length (not aln len) commit | commitdiff | tree | snapshot
2012-03-24 Heng Limove seqtk to a separate project commit | commitdiff | tree | snapshot
2012-03-23 peterjcCorrect my error message; assed some comments commit | commitdiff | tree | snapshot
2012-03-23 peterjcAdd TODO note about reference lengths commit | commitdiff | tree | snapshot
2012-03-23 peterjcCope with CIGAR D or P to mark gaps in an embedded... commit | commitdiff | tree | snapshot
2012-03-22 peterjcCheck current reference sequence matches RNAME in samto... commit | commitdiff | tree | snapshot
2012-03-22 peterjcSupport CIGAR X/= in depad commit | commitdiff | tree | snapshot
2012-03-22 peterjcHelpful error message on bad CIGAR in unpad_seq commit | commitdiff | tree | snapshot
2012-03-22 Heng Lichange SO commit | commitdiff | tree | snapshot
2012-03-22 Heng Lia little more accurate mem estimate commit | commitdiff | tree | snapshot
2012-03-22 Heng Licontrol compression level at command line commit | commitdiff | tree | snapshot
2012-03-20 Heng Lioptionally surpress /[12] in bam2fq commit | commitdiff | tree | snapshot
2012-03-20 Heng LiMerge branch 'master' into mt commit | commitdiff | tree | snapshot
2012-03-20 Heng Libugfix: downsampling not always working commit | commitdiff | tree | snapshot
2012-03-19 Heng Liname sorting checkes READ1 and READ2 commit | commitdiff | tree | snapshot
2012-03-19 Heng Lisorting also considers strand commit | commitdiff | tree | snapshot
2012-03-18 Heng Lichange the default block size in sorting commit | commitdiff | tree | snapshot
2012-03-18 Heng Limulti-threaded sorting commit | commitdiff | tree | snapshot
2012-03-18 Heng Liadded .gitignore commit | commitdiff | tree | snapshot
2012-03-18 Heng Liadded mt comression to merge commit | commitdiff | tree | snapshot
2012-03-18 Heng Liupdated the alphanum comparison function commit | commitdiff | tree | snapshot
2012-03-18 Heng Liavoid wasting CPU time by the master thread commit | commitdiff | tree | snapshot
2012-03-18 Heng Liuse conditional variable commit | commitdiff | tree | snapshot
2012-03-18 Heng Libugfix in caching commit | commitdiff | tree | snapshot
2012-03-18 Heng Limulti-threading working on toy examples commit | commitdiff | tree | snapshot
2012-03-18 Heng Lipreliminary implementation; not tested commit | commitdiff | tree | snapshot
2012-03-18 Heng Liupdated with the latest bgzf library commit | commitdiff | tree | snapshot
2012-03-09 Heng LiOn behalf of Petr: multi-allelic GT commit | commitdiff | tree | snapshot
2012-03-09 Heng LiRemoved SVN ChangeLog; merged my private github Log... commit | commitdiff | tree | snapshot
2012-03-09 Heng Lidoc for downsampling commit | commitdiff | tree | snapshot
2012-03-09 Heng Lianother example, used by g1k for QA commit | commitdiff | tree | snapshot
2012-03-09 Heng LiTwo auxilary Lua scripts commit | commitdiff | tree | snapshot
2012-03-09 Heng LiIncoporated changes from Nils Homer. commit | commitdiff | tree | snapshot
2012-02-16 Heng Libugfix: wrong SP; missing DV in the VCF header commit | commitdiff | tree | snapshot
2012-02-08 Heng Lichanges from git commit | commitdiff | tree | snapshot
2011-09-28 Heng Liunpadded output commit | commitdiff | tree | snapshot
2011-09-23 Heng Liadded the ace2sam converter commit | commitdiff | tree | snapshot
2011-09-23 Heng Liconverted padded SAM to unpadded SAM commit | commitdiff | tree | snapshot
2011-09-02 Heng Li * Updated samtools to the latest commit | commitdiff | tree | snapshot
2011-08-17 Heng Li * bugfix in index: large memory when a read pos is 1 commit | commitdiff | tree | snapshot
2011-07-15 Heng Liallow to set seed in view-subsampling commit | commitdiff | tree | snapshot
2011-07-15 Heng Lisubsampling read pairs commit | commitdiff | tree | snapshot
2011-07-13 Heng Lisupport trio indels commit | commitdiff | tree | snapshot
2011-07-07 Heng Lifor WIN32 compatibility commit | commitdiff | tree | snapshot
2011-07-07 Heng Lifixed a bug in bam_plcmd.c commit | commitdiff | tree | snapshot
2011-07-07 Heng LiRelease samtools-0.1.17 commit | commitdiff | tree | snapshot
2011-06-15 Heng Lifixed a bug caused by a recent patch commit | commitdiff | tree | snapshot
2011-06-03 Heng Li * 0.1.16-dev (r969:252) commit | commitdiff | tree | snapshot
2011-04-22 Heng LiRemoved the pileup command commit | commitdiff | tree | snapshot
2011-04-22 Heng LiRelease samtools-0.1.16 (r963:234) commit | commitdiff | tree | snapshot
2011-04-21 Heng Lifixed a bug in merge commit | commitdiff | tree | snapshot
2011-04-18 Heng LiAdded the support for the new SAM/BAM type "B" commit | commitdiff | tree | snapshot
2011-04-17 Heng Li * fixed a bug in bedidx: input BED not sorted commit | commitdiff | tree | snapshot
2011-04-15 Heng Li * Added Brent's method for frequency estimate commit | commitdiff | tree | snapshot
2011-04-10 Heng LiRelease samtools-0.1.15 (r949:203) commit | commitdiff | tree | snapshot
2011-04-08 Heng Li * added bam_verbose global variable commit | commitdiff | tree | snapshot
2011-04-01 Heng Liadded quality filtering commit | commitdiff | tree | snapshot
2011-04-01 Heng Lifixed a few typos in comments commit | commitdiff | tree | snapshot
2011-04-01 Heng LiAdded an example of using mpileup commit | commitdiff | tree | snapshot
2011-03-31 Heng Li * synchronize bgzf in tabix and in samtools commit | commitdiff | tree | snapshot
2011-03-30 Heng Li * added BED support to samtools view and mpileup and... commit | commitdiff | tree | snapshot
2011-03-22 Heng LiRelease samtools-0.1.14 (r933:170) commit | commitdiff | tree | snapshot
2011-03-18 Heng Liforget to add this file commit | commitdiff | tree | snapshot
2011-03-18 Heng Li * allow to change the compression level in BAM output commit | commitdiff | tree | snapshot
2011-03-18 Heng Liexport2sam.pl-2.3.1, provided by Chris Saunders from... commit | commitdiff | tree | snapshot
2011-03-08 Heng Liadded the haploid mode commit | commitdiff | tree | snapshot
2011-03-01 Heng LiRelease samtools-0.1.13 (r926:134) commit | commitdiff | tree | snapshot
2011-03-01 Heng Li * optionally drop phase ambiguous reads commit | commitdiff | tree | snapshot
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