samtools.git
2013-04-29 pd3Merge pull request #44 from peterjc/check_bins master
2013-04-24 peterjcCorrect BIN check for CIGAR less reads
2013-04-24 peterjcShow reference name in bad BIN error message
2013-04-23 pd3Merge pull request #43 from peterjc/depad_bins
2013-04-19 peterjcSlightly more detailed error message for debugging.
2013-04-19 peterjcShould update POS on unmapped reads in 'samtools depad'
2013-04-19 peterjcUpdate 'samtools depad' help text regarding FASTA refer...
2013-04-19 peterjcVerify old BIN value of reads during 'samtools index'.
2013-04-19 peterjcUpdate BIN values in 'samtools depad'
2013-04-05 Petr Danecekbgzip now compiles
2013-03-26 Petr DanecekThe indel stats (IS) annotation splitted into two:...
2013-03-20 Petr Danecekmpileup indel hotfix: fix in detecting long stretches...
2013-03-20 Petr Danecekmpileup fix: Print error message and exit when no files...
2013-03-18 Petr Danecekbcftools: version bump
2013-03-15 Petr DanecekVersion bump
2013-03-15 Petr DanecekUpdated NEWS document
2013-03-15 Petr DanecekMerge remote branch 'pd3master/master'
2013-03-15 Petr DanecekGet rid of %ld-with-int64_t warning on Mac
2013-03-15 Petr DanecekUpdated man pages
2013-03-15 Petr Danecekmpileup: New HWE, QBD, RPS annotations. Modified VDB...
2013-03-12 Petr DanecekFixed brackets missing in the previous commit
2013-03-12 Petr DanecekMerge remote branch 'remotes/master/master' into fb...
2013-03-12 Petr Danecekbackup commit
2013-03-12 Petr DanecekMerge branch 'master' of github.com:samtools/samtools
2013-03-12 Petr Danecekbcftools view: Exit with an error if the -l file cannot...
2013-03-10 Heng LiMerge pull request #30 from leecbaker/master
2013-03-09 Lee BakerFix memory leaks:
2013-03-07 Petr Danecekbackup commit
2013-03-01 Petr Danecekbcftools view: always output the header, even when...
2013-02-27 Manuel HoltgreweAdding -f flag to samtools sort to give output name...
2013-01-28 Petr DanecekMerge remote branch 'remotes/pierre/master' into develop
2013-01-25 lindenbfix html
2013-01-25 lindenbcont
2013-01-25 lindenbworks
2013-01-25 lindenbcont
2013-01-25 lindenbworks with curses
2013-01-25 Pierre Lindenbaumcont
2013-01-24 Pierre Lindenbaum...
2013-01-07 Heng Lidump log-likelihood
2013-01-03 Petr Danecekbamcheck: new stats, number of filtered vs raw sequences
2012-12-13 Petr DanecekMerge branch 'vsbuffalo-master' into develop
2012-12-13 Vince Buffalofixed missing braces
2012-12-13 Vince Buffalobig fix: using samtools view file.bam gibberish returns...
2012-12-12 Petr Danecekmpileup: New --rf and --ff options for filtering reads
2012-12-12 Petr Danecekbamcheck: New stats - the number of QC failed reads...
2012-12-12 Petr Danecekbam2depth: Enabled reading the list of BAMs from a...
2012-12-11 Petr Danecekksort.h: declared __ks_insertsort_##name as static...
2012-12-03 Petr Danecekbam_plcmd.c: more descriptive -b usage help message
2012-12-03 Petr Danecekbam_plcmd.c: added sanity check in read_file_list,...
2012-12-03 Petr Danecekbamcheck: New stats, number of pairs mapped to differen...
2012-11-27 Petr Danecekmisc/Makefile, on behalf of ghuls: changed the order...
2012-11-27 Petr Danecekbamcheck: max quality value increased to 255 to handle...
2012-11-22 Petr Danecekbamcheck: Fixed a bug introduced by previous change...
2012-11-15 Petr DanecekMerge remote branch 'remotes/pd3master/master' into...
2012-11-09 Petr DanecekDrop empty bins from coverage distribution
2012-11-09 Petr DanecekChanged default reflen; more informative error message...
2012-10-11 Petr DanecekMore user-friendly error output
2012-10-10 Petr DanecekComplain when BAM cannot be open. Severe bug fixed...
2012-09-12 Petr DanecekMerge remote branch 'remotes/pd3/master'
2012-09-05 Petr DanecekFix in insertion cycle calculation of rev reads
2012-09-05 Petr DanecekGC-depth calculation now more robust to small GCD bin...
2012-09-04 Petr DanecekNew --GC-depth option to bamcheck. Take into account...
2012-08-21 Heng LiMerge pull request #14 from peterjc/depad3
2012-08-17 peterjcFix 'samtools depad' seg-fault when MPOS/PNEXT given...
2012-08-17 peterjcTweak order free things (avoids an 'samtools depad...
2012-08-17 peterjcFirst attempt at updating MPOS in 'samtools depad'
2012-08-03 Heng Lir580: bugfix - bam_aux_get() error given 'f' type
2012-08-02 Petr DanecekUse int64_t to prevent count overflow in view -c; on...
2012-07-18 Petr DanecekFix in output of missing haploid genotypes
2012-07-05 Petr DanecekAllow filtering by read group or sample name in bamchec...
2012-07-05 Petr DanecekVCF annotations with and without -m and more robust...
2012-07-03 Petr DanecekBug fixes
2012-07-02 Petr DanecekAlternative model for multiallelic and rare-variant...
2012-06-27 Petr DanecekNew -p switch for increased sensititivy of indel-callin...
2012-06-21 Petr DanecekMerge branch 'master' of github.com:samtools/samtools
2012-06-21 Petr DanecekNew -p option to start tview at desired position
2012-06-19 Heng Lir579: after merging Peter's depad changes
2012-06-19 Heng Lifixed a couple of minor compiling warnings
2012-06-19 Heng LiMerge pull request #11 from peterjc/depad2
2012-06-19 peterjcUpdate @SQ lines during 'samtools depad'
2012-06-19 peterjcCalculate unpadded reference length, update BAM header...
2012-06-19 peterjcSAM/BAM input to 'samtools depad' not linked to FASTA...
2012-06-19 peterjcWording of error messages
2012-06-19 peterjcCatch missing reference error in faidx (avoids floating...
2012-06-19 peterjcCheck embedded reference against FASTA if given in...
2012-06-19 peterjcUse FASTA file when no embedded reference in 'samtools...
2012-06-19 peterjcLoad FAI in 'samtools depad' (not used yet)
2012-06-19 peterjcAdd reference FASTA file to 'samtools depad' command...
2012-06-19 peterjcSupport SAM or BAM input/output in 'samtools depad...
2012-06-19 peterjcMinimal 'samtools depad' command line parsing (-? only...
2012-06-19 peterjcAdding a usage function to 'samtools depad' following...
2012-06-19 peterjcAdd a tiny bit of help text to 'samtools depad' command.
2012-06-19 peterjcRevert one of my earlier changes - Heng was right,...
2012-06-19 peterjcFix buffer overflow in 'samtools depad' with CIGAR...
2012-06-19 peterjcFixed the next silly error on that line.
2012-06-19 peterjcFix silly typo
2012-06-19 peterjcMore elegant solution to avoid superfluous leading...
2012-06-19 peterjcRefine logic for removing superfluous P ops (still...
2012-06-12 Petr DanecekMerge remote branch 'rq/getopt_mac'
2012-06-12 peterjcFix missing declaration for getopt on Mac OS X
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