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samtools.git
2013-04-29 pd3Merge pull request #44 from peterjc/check_bins master commit | commitdiff | tree | snapshot
2013-04-24 peterjcCorrect BIN check for CIGAR less reads commit | commitdiff | tree | snapshot
2013-04-24 peterjcShow reference name in bad BIN error message commit | commitdiff | tree | snapshot
2013-04-23 pd3Merge pull request #43 from peterjc/depad_bins commit | commitdiff | tree | snapshot
2013-04-19 peterjcSlightly more detailed error message for debugging. commit | commitdiff | tree | snapshot
2013-04-19 peterjcShould update POS on unmapped reads in 'samtools depad' commit | commitdiff | tree | snapshot
2013-04-19 peterjcUpdate 'samtools depad' help text regarding FASTA refer... commit | commitdiff | tree | snapshot
2013-04-19 peterjcVerify old BIN value of reads during 'samtools index'. commit | commitdiff | tree | snapshot
2013-04-19 peterjcUpdate BIN values in 'samtools depad' commit | commitdiff | tree | snapshot
2013-04-05 Petr Danecekbgzip now compiles commit | commitdiff | tree | snapshot
2013-03-26 Petr DanecekThe indel stats (IS) annotation splitted into two:... commit | commitdiff | tree | snapshot
2013-03-20 Petr Danecekmpileup indel hotfix: fix in detecting long stretches... commit | commitdiff | tree | snapshot
2013-03-20 Petr Danecekmpileup fix: Print error message and exit when no files... commit | commitdiff | tree | snapshot
2013-03-18 Petr Danecekbcftools: version bump commit | commitdiff | tree | snapshot
2013-03-15 Petr DanecekVersion bump commit | commitdiff | tree | snapshot
2013-03-15 Petr DanecekUpdated NEWS document commit | commitdiff | tree | snapshot
2013-03-15 Petr DanecekMerge remote branch 'pd3master/master' commit | commitdiff | tree | snapshot
2013-03-15 Petr DanecekGet rid of %ld-with-int64_t warning on Mac commit | commitdiff | tree | snapshot
2013-03-15 Petr DanecekUpdated man pages commit | commitdiff | tree | snapshot
2013-03-15 Petr Danecekmpileup: New HWE, QBD, RPS annotations. Modified VDB... commit | commitdiff | tree | snapshot
2013-03-12 Petr DanecekFixed brackets missing in the previous commit commit | commitdiff | tree | snapshot
2013-03-12 Petr DanecekMerge remote branch 'remotes/master/master' into fb... commit | commitdiff | tree | snapshot
2013-03-12 Petr Danecekbackup commit commit | commitdiff | tree | snapshot
2013-03-12 Petr DanecekMerge branch 'master' of github.com:samtools/samtools commit | commitdiff | tree | snapshot
2013-03-12 Petr Danecekbcftools view: Exit with an error if the -l file cannot... commit | commitdiff | tree | snapshot
2013-03-10 Heng LiMerge pull request #30 from leecbaker/master commit | commitdiff | tree | snapshot
2013-03-09 Lee BakerFix memory leaks: commit | commitdiff | tree | snapshot
2013-03-07 Petr Danecekbackup commit commit | commitdiff | tree | snapshot
2013-03-01 Petr Danecekbcftools view: always output the header, even when... commit | commitdiff | tree | snapshot
2013-02-27 Manuel HoltgreweAdding -f flag to samtools sort to give output name... commit | commitdiff | tree | snapshot
2013-01-28 Petr DanecekMerge remote branch 'remotes/pierre/master' into develop commit | commitdiff | tree | snapshot
2013-01-25 lindenbfix html commit | commitdiff | tree | snapshot
2013-01-25 lindenbcont commit | commitdiff | tree | snapshot
2013-01-25 lindenbworks commit | commitdiff | tree | snapshot
2013-01-25 lindenbcont commit | commitdiff | tree | snapshot
2013-01-25 lindenbworks with curses commit | commitdiff | tree | snapshot
2013-01-25 Pierre Lindenbaumcont commit | commitdiff | tree | snapshot
2013-01-24 Pierre Lindenbaum... commit | commitdiff | tree | snapshot
2013-01-07 Heng Lidump log-likelihood commit | commitdiff | tree | snapshot
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
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