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samtools.git
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
2011-02-28 Heng Liminor changes to a heuristic rule commit | commitdiff | tree | snapshot
2011-02-28 Heng Li * 0.1.12-r924:126 commit | commitdiff | tree | snapshot
2011-02-28 Heng Li * put version number in bam.h commit | commitdiff | tree | snapshot
2011-02-25 Heng Li * change the order of PL/GL according to the latest... commit | commitdiff | tree | snapshot
2011-02-25 Heng Liupdate the BCF spec commit | commitdiff | tree | snapshot
2011-02-25 Heng Liadded the phase command commit | commitdiff | tree | snapshot
2011-02-24 Heng Liadded "const" to bcf_p1_cal() commit | commitdiff | tree | snapshot
2011-02-24 Heng Limore meaningful BAM truncation message commit | commitdiff | tree | snapshot
2011-02-24 Heng Li * automatically fix errors in GL commit | commitdiff | tree | snapshot
2011-02-11 Heng Lifinished VCF->BCF conversion commit | commitdiff | tree | snapshot
2011-02-03 Petr DanecekPrevent division by zero commit | commitdiff | tree | snapshot
2011-02-02 Heng Lifixed a typo in the VCF header commit | commitdiff | tree | snapshot
2011-02-02 Heng Li * fixed an out-of-boundary bug commit | commitdiff | tree | snapshot
2011-01-30 Heng Li * avoid a segfault when network connect fails commit | commitdiff | tree | snapshot
2011-01-27 Heng Li * fixed a rare memory issue in bam_md.c commit | commitdiff | tree | snapshot
2011-01-24 Heng Lifixed two minor bugs in Fisher's exact test commit | commitdiff | tree | snapshot
2011-01-19 Petr DanecekSkip sites with unknown ref commit | commitdiff | tree | snapshot
2011-01-15 Heng Limove bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c commit | commitdiff | tree | snapshot
2011-01-06 Heng Li * samtools-0.1.12-10 (r896) commit | commitdiff | tree | snapshot
2011-01-04 Heng Lisorry. It is SP not ST commit | commitdiff | tree | snapshot
2011-01-04 Heng Liadded ST commit | commitdiff | tree | snapshot
2011-01-04 Petr DanecekFixed a typo in read_samples commit | commitdiff | tree | snapshot
2010-12-28 On behalf of... System libraries go *after* user libraries in link... commit | commitdiff | tree | snapshot
2010-12-21 Heng Li * samtools-0.1.12-9 (r891) commit | commitdiff | tree | snapshot
2010-12-15 Heng Li * samtools-0.1.12-12 (r889) commit | commitdiff | tree | snapshot
2010-12-15 Heng LiWhen -B is applied to mpileup, still use paired reads... commit | commitdiff | tree | snapshot
2010-12-15 Heng Li * samtools-0.1.12-6 (r887) commit | commitdiff | tree | snapshot
2010-12-14 Heng Li(Arguably) improved the indel caller a tiny bit for... commit | commitdiff | tree | snapshot
2010-12-14 Petr DanecekFixed the VCF header to pass validation commit | commitdiff | tree | snapshot
2010-12-13 Heng Li * samtools-0.1.12-4 (r884) commit | commitdiff | tree | snapshot
2010-12-12 Heng Licompute max SP and max GQ from sample genotypes commit | commitdiff | tree | snapshot
2010-12-10 Heng Lidrop bcf-fix.pl as it is redundant by the latest changes commit | commitdiff | tree | snapshot
2010-12-10 Heng Li * fixed a minor issue in printing VCFs commit | commitdiff | tree | snapshot
2010-12-10 Heng LiMake sure that the GT genotype field is the first commit | commitdiff | tree | snapshot
2010-12-08 Heng Li * samtools-0.1.12-2 (r877) commit | commitdiff | tree | snapshot
2010-12-08 Heng Lia spelling error.. commit | commitdiff | tree | snapshot
2010-12-08 Heng Li * samtools-0.1.12-1 (r873) commit | commitdiff | tree | snapshot
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