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samtools.git
2013-01-03 Petr Danecekbamcheck: new stats, number of filtered vs raw sequences commit | commitdiff | tree | snapshot
2012-12-13 Petr DanecekMerge branch 'vsbuffalo-master' into develop commit | commitdiff | tree | snapshot
2012-12-13 Vince Buffalofixed missing braces commit | commitdiff | tree | snapshot
2012-12-13 Vince Buffalobig fix: using samtools view file.bam gibberish returns... commit | commitdiff | tree | snapshot
2012-12-12 Petr Danecekmpileup: New --rf and --ff options for filtering reads commit | commitdiff | tree | snapshot
2012-12-12 Petr Danecekbamcheck: New stats - the number of QC failed reads... commit | commitdiff | tree | snapshot
2012-12-12 Petr Danecekbam2depth: Enabled reading the list of BAMs from a... commit | commitdiff | tree | snapshot
2012-12-11 Petr Danecekksort.h: declared __ks_insertsort_##name as static... commit | commitdiff | tree | snapshot
2012-12-03 Petr Danecekbam_plcmd.c: more descriptive -b usage help message commit | commitdiff | tree | snapshot
2012-12-03 Petr Danecekbam_plcmd.c: added sanity check in read_file_list,... commit | commitdiff | tree | snapshot
2012-12-03 Petr Danecekbamcheck: New stats, number of pairs mapped to differen... commit | commitdiff | tree | snapshot
2012-11-27 Petr Danecekmisc/Makefile, on behalf of ghuls: changed the order... commit | commitdiff | tree | snapshot
2012-11-27 Petr Danecekbamcheck: max quality value increased to 255 to handle... commit | commitdiff | tree | snapshot
2012-11-22 Petr Danecekbamcheck: Fixed a bug introduced by previous change... commit | commitdiff | tree | snapshot
2012-11-15 Petr DanecekMerge remote branch 'remotes/pd3master/master' into... commit | commitdiff | tree | snapshot
2012-11-09 Petr DanecekDrop empty bins from coverage distribution commit | commitdiff | tree | snapshot
2012-11-09 Petr DanecekChanged default reflen; more informative error message... commit | commitdiff | tree | snapshot
2012-10-11 Petr DanecekMore user-friendly error output commit | commitdiff | tree | snapshot
2012-10-10 Petr DanecekComplain when BAM cannot be open. Severe bug fixed... commit | commitdiff | tree | snapshot
2012-09-12 Petr DanecekMerge remote branch 'remotes/pd3/master' commit | commitdiff | tree | snapshot
2012-09-05 Petr DanecekFix in insertion cycle calculation of rev reads commit | commitdiff | tree | snapshot
2012-09-05 Petr DanecekGC-depth calculation now more robust to small GCD bin... commit | commitdiff | tree | snapshot
2012-09-04 Petr DanecekNew --GC-depth option to bamcheck. Take into account... commit | commitdiff | tree | snapshot
2012-08-21 Heng LiMerge pull request #14 from peterjc/depad3 commit | commitdiff | tree | snapshot
2012-08-17 peterjcFix 'samtools depad' seg-fault when MPOS/PNEXT given... commit | commitdiff | tree | snapshot
2012-08-17 peterjcTweak order free things (avoids an 'samtools depad... commit | commitdiff | tree | snapshot
2012-08-17 peterjcFirst attempt at updating MPOS in 'samtools depad' commit | commitdiff | tree | snapshot
2012-08-03 Heng Lir580: bugfix - bam_aux_get() error given 'f' type commit | commitdiff | tree | snapshot
2012-08-02 Petr DanecekUse int64_t to prevent count overflow in view -c; on... commit | commitdiff | tree | snapshot
2012-07-18 Petr DanecekFix in output of missing haploid genotypes commit | commitdiff | tree | snapshot
2012-07-05 Petr DanecekAllow filtering by read group or sample name in bamchec... commit | commitdiff | tree | snapshot
2012-07-05 Petr DanecekVCF annotations with and without -m and more robust... commit | commitdiff | tree | snapshot
2012-07-03 Petr DanecekBug fixes commit | commitdiff | tree | snapshot
2012-07-02 Petr DanecekAlternative model for multiallelic and rare-variant... commit | commitdiff | tree | snapshot
2012-06-27 Petr DanecekNew -p switch for increased sensititivy of indel-callin... commit | commitdiff | tree | snapshot
2012-06-21 Petr DanecekMerge branch 'master' of github.com:samtools/samtools commit | commitdiff | tree | snapshot
2012-06-21 Petr DanecekNew -p option to start tview at desired position commit | commitdiff | tree | snapshot
2012-06-19 Heng Lir579: after merging Peter's depad changes commit | commitdiff | tree | snapshot
2012-06-19 Heng Lifixed a couple of minor compiling warnings commit | commitdiff | tree | snapshot
2012-06-19 Heng LiMerge pull request #11 from peterjc/depad2 commit | commitdiff | tree | snapshot
2012-06-19 peterjcUpdate @SQ lines during 'samtools depad' commit | commitdiff | tree | snapshot
2012-06-19 peterjcCalculate unpadded reference length, update BAM header... commit | commitdiff | tree | snapshot
2012-06-19 peterjcSAM/BAM input to 'samtools depad' not linked to FASTA... commit | commitdiff | tree | snapshot
2012-06-19 peterjcWording of error messages commit | commitdiff | tree | snapshot
2012-06-19 peterjcCatch missing reference error in faidx (avoids floating... commit | commitdiff | tree | snapshot
2012-06-19 peterjcCheck embedded reference against FASTA if given in... commit | commitdiff | tree | snapshot
2012-06-19 peterjcUse FASTA file when no embedded reference in 'samtools... commit | commitdiff | tree | snapshot
2012-06-19 peterjcLoad FAI in 'samtools depad' (not used yet) commit | commitdiff | tree | snapshot
2012-06-19 peterjcAdd reference FASTA file to 'samtools depad' command... commit | commitdiff | tree | snapshot
2012-06-19 peterjcSupport SAM or BAM input/output in 'samtools depad... commit | commitdiff | tree | snapshot
2012-06-19 peterjcMinimal 'samtools depad' command line parsing (-? only... commit | commitdiff | tree | snapshot
2012-06-19 peterjcAdding a usage function to 'samtools depad' following... commit | commitdiff | tree | snapshot
2012-06-19 peterjcAdd a tiny bit of help text to 'samtools depad' command. commit | commitdiff | tree | snapshot
2012-06-19 peterjcRevert one of my earlier changes - Heng was right,... commit | commitdiff | tree | snapshot
2012-06-19 peterjcFix buffer overflow in 'samtools depad' with CIGAR... commit | commitdiff | tree | snapshot
2012-06-19 peterjcFixed the next silly error on that line. commit | commitdiff | tree | snapshot
2012-06-19 peterjcFix silly typo commit | commitdiff | tree | snapshot
2012-06-19 peterjcMore elegant solution to avoid superfluous leading... commit | commitdiff | tree | snapshot
2012-06-19 peterjcRefine logic for removing superfluous P ops (still... commit | commitdiff | tree | snapshot
2012-06-12 Petr DanecekMerge remote branch 'rq/getopt_mac' commit | commitdiff | tree | snapshot
2012-06-12 peterjcFix missing declaration for getopt on Mac OS X commit | commitdiff | tree | snapshot
2012-06-07 kortschakUpdate bam1_core_t and bam1_t documentation commit | commitdiff | tree | snapshot
2012-06-07 Petr DanecekNew -s option for multisample BAMs: include only reads... commit | commitdiff | tree | snapshot
2012-05-30 Petr DanecekFixed errors introduced by the 8c15f916dabce475febdf508... commit | commitdiff | tree | snapshot
2012-05-25 Petr DanecekThe -E switch to recalculate extended BAQ on the fly... commit | commitdiff | tree | snapshot
2012-05-25 Petr DanecekFix to prevent long stretches of Ns to be mistaken... commit | commitdiff | tree | snapshot
2012-05-18 Petr DanecekMerge branch 'master' of github.com:samtools/samtools commit | commitdiff | tree | snapshot
2012-05-18 Petr DanecekAdded -f, -F options. Count and plot indels per cycle... commit | commitdiff | tree | snapshot
2012-05-17 Heng Lichange the default clevel to 1 for speed commit | commitdiff | tree | snapshot
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
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