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2013-03-12	Petr Danecek	Merge remote branch 'remotes/master/master' into fb...	commit \| commitdiff \| tree \| snapshot
2013-03-12	Petr Danecek	backup commit	commit \| commitdiff \| tree \| snapshot
2013-03-12	Petr Danecek	Merge branch 'master' of github.com:samtools/samtools	commit \| commitdiff \| tree \| snapshot
2013-03-12	Petr Danecek	bcftools view: Exit with an error if the -l file cannot...	commit \| commitdiff \| tree \| snapshot
2013-03-10	Heng Li	Merge pull request #30 from leecbaker/master	commit \| commitdiff \| tree \| snapshot
2013-03-09	Lee Baker	Fix memory leaks:	commit \| commitdiff \| tree \| snapshot
2013-03-07	Petr Danecek	backup commit	commit \| commitdiff \| tree \| snapshot
2013-03-01	Petr Danecek	bcftools view: always output the header, even when...	commit \| commitdiff \| tree \| snapshot
2013-02-27	Manuel Holtgrewe	Adding -f flag to samtools sort to give output name...	commit \| commitdiff \| tree \| snapshot
2013-01-28	Petr Danecek	Merge remote branch 'remotes/pierre/master' into develop	commit \| commitdiff \| tree \| snapshot
2013-01-25	lindenb	fix html	commit \| commitdiff \| tree \| snapshot
2013-01-25	lindenb	cont	commit \| commitdiff \| tree \| snapshot
2013-01-25	lindenb	works	commit \| commitdiff \| tree \| snapshot
2013-01-25	lindenb	cont	commit \| commitdiff \| tree \| snapshot
2013-01-25	lindenb	works with curses	commit \| commitdiff \| tree \| snapshot
2013-01-25	Pierre Lindenbaum	cont	commit \| commitdiff \| tree \| snapshot
2013-01-24	Pierre Lindenbaum	...	commit \| commitdiff \| tree \| snapshot
2013-01-07	Heng Li	dump log-likelihood	commit \| commitdiff \| tree \| snapshot
2013-01-03	Petr Danecek	bamcheck: new stats, number of filtered vs raw sequences	commit \| commitdiff \| tree \| snapshot
2012-12-13	Petr Danecek	Merge branch 'vsbuffalo-master' into develop	commit \| commitdiff \| tree \| snapshot
2012-12-13	Vince Buffalo	fixed missing braces	commit \| commitdiff \| tree \| snapshot
2012-12-13	Vince Buffalo	big fix: using samtools view file.bam gibberish returns...	commit \| commitdiff \| tree \| snapshot
2012-12-12	Petr Danecek	mpileup: New --rf and --ff options for filtering reads	commit \| commitdiff \| tree \| snapshot
2012-12-12	Petr Danecek	bamcheck: New stats - the number of QC failed reads...	commit \| commitdiff \| tree \| snapshot
2012-12-12	Petr Danecek	bam2depth: Enabled reading the list of BAMs from a...	commit \| commitdiff \| tree \| snapshot
2012-12-11	Petr Danecek	ksort.h: declared __ks_insertsort_##name as static...	commit \| commitdiff \| tree \| snapshot
2012-12-03	Petr Danecek	bam_plcmd.c: more descriptive -b usage help message	commit \| commitdiff \| tree \| snapshot
2012-12-03	Petr Danecek	bam_plcmd.c: added sanity check in read_file_list,...	commit \| commitdiff \| tree \| snapshot
2012-12-03	Petr Danecek	bamcheck: New stats, number of pairs mapped to differen...	commit \| commitdiff \| tree \| snapshot
2012-11-27	Petr Danecek	misc/Makefile, on behalf of ghuls: changed the order...	commit \| commitdiff \| tree \| snapshot
2012-11-27	Petr Danecek	bamcheck: max quality value increased to 255 to handle...	commit \| commitdiff \| tree \| snapshot
2012-11-22	Petr Danecek	bamcheck: Fixed a bug introduced by previous change...	commit \| commitdiff \| tree \| snapshot
2012-11-15	Petr Danecek	Merge remote branch 'remotes/pd3master/master' into...	commit \| commitdiff \| tree \| snapshot
2012-11-09	Petr Danecek	Drop empty bins from coverage distribution	commit \| commitdiff \| tree \| snapshot
2012-11-09	Petr Danecek	Changed default reflen; more informative error message...	commit \| commitdiff \| tree \| snapshot
2012-10-11	Petr Danecek	More user-friendly error output	commit \| commitdiff \| tree \| snapshot
2012-10-10	Petr Danecek	Complain when BAM cannot be open. Severe bug fixed...	commit \| commitdiff \| tree \| snapshot
2012-09-12	Petr Danecek	Merge remote branch 'remotes/pd3/master'	commit \| commitdiff \| tree \| snapshot
2012-09-05	Petr Danecek	Fix in insertion cycle calculation of rev reads	commit \| commitdiff \| tree \| snapshot
2012-09-05	Petr Danecek	GC-depth calculation now more robust to small GCD bin...	commit \| commitdiff \| tree \| snapshot
2012-09-04	Petr Danecek	New --GC-depth option to bamcheck. Take into account...	commit \| commitdiff \| tree \| snapshot
2012-08-21	Heng Li	Merge pull request #14 from peterjc/depad3	commit \| commitdiff \| tree \| snapshot
2012-08-17	peterjc	Fix 'samtools depad' seg-fault when MPOS/PNEXT given...	commit \| commitdiff \| tree \| snapshot
2012-08-17	peterjc	Tweak order free things (avoids an 'samtools depad...	commit \| commitdiff \| tree \| snapshot
2012-08-17	peterjc	First attempt at updating MPOS in 'samtools depad'	commit \| commitdiff \| tree \| snapshot
2012-08-03	Heng Li	r580: bugfix - bam_aux_get() error given 'f' type	commit \| commitdiff \| tree \| snapshot
2012-08-02	Petr Danecek	Use int64_t to prevent count overflow in view -c; on...	commit \| commitdiff \| tree \| snapshot
2012-07-18	Petr Danecek	Fix in output of missing haploid genotypes	commit \| commitdiff \| tree \| snapshot
2012-07-05	Petr Danecek	Allow filtering by read group or sample name in bamchec...	commit \| commitdiff \| tree \| snapshot
2012-07-05	Petr Danecek	VCF annotations with and without -m and more robust...	commit \| commitdiff \| tree \| snapshot
2012-07-03	Petr Danecek	Bug fixes	commit \| commitdiff \| tree \| snapshot
2012-07-02	Petr Danecek	Alternative model for multiallelic and rare-variant...	commit \| commitdiff \| tree \| snapshot
2012-06-27	Petr Danecek	New -p switch for increased sensititivy of indel-callin...	commit \| commitdiff \| tree \| snapshot
2012-06-21	Petr Danecek	Merge branch 'master' of github.com:samtools/samtools	commit \| commitdiff \| tree \| snapshot
2012-06-21	Petr Danecek	New -p option to start tview at desired position	commit \| commitdiff \| tree \| snapshot
2012-06-19	Heng Li	r579: after merging Peter's depad changes	commit \| commitdiff \| tree \| snapshot
2012-06-19	Heng Li	fixed a couple of minor compiling warnings	commit \| commitdiff \| tree \| snapshot
2012-06-19	Heng Li	Merge pull request #11 from peterjc/depad2	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Update @SQ lines during 'samtools depad'	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Calculate unpadded reference length, update BAM header...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	SAM/BAM input to 'samtools depad' not linked to FASTA...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Wording of error messages	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Catch missing reference error in faidx (avoids floating...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Check embedded reference against FASTA if given in...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Use FASTA file when no embedded reference in 'samtools...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Load FAI in 'samtools depad' (not used yet)	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Add reference FASTA file to 'samtools depad' command...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Support SAM or BAM input/output in 'samtools depad...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Minimal 'samtools depad' command line parsing (-? only...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Adding a usage function to 'samtools depad' following...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Add a tiny bit of help text to 'samtools depad' command.	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Revert one of my earlier changes - Heng was right,...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Fix buffer overflow in 'samtools depad' with CIGAR...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Fixed the next silly error on that line.	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Fix silly typo	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	More elegant solution to avoid superfluous leading...	commit \| commitdiff \| tree \| snapshot
2012-06-19	peterjc	Refine logic for removing superfluous P ops (still...	commit \| commitdiff \| tree \| snapshot
2012-06-12	Petr Danecek	Merge remote branch 'rq/getopt_mac'	commit \| commitdiff \| tree \| snapshot
2012-06-12	peterjc	Fix missing declaration for getopt on Mac OS X	commit \| commitdiff \| tree \| snapshot
2012-06-07	kortschak	Update bam1_core_t and bam1_t documentation	commit \| commitdiff \| tree \| snapshot
2012-06-07	Petr Danecek	New -s option for multisample BAMs: include only reads...	commit \| commitdiff \| tree \| snapshot
2012-05-30	Petr Danecek	Fixed errors introduced by the 8c15f916dabce475febdf508...	commit \| commitdiff \| tree \| snapshot
2012-05-25	Petr Danecek	The -E switch to recalculate extended BAQ on the fly...	commit \| commitdiff \| tree \| snapshot
2012-05-25	Petr Danecek	Fix to prevent long stretches of Ns to be mistaken...	commit \| commitdiff \| tree \| snapshot
2012-05-18	Petr Danecek	Merge branch 'master' of github.com:samtools/samtools	commit \| commitdiff \| tree \| snapshot
2012-05-18	Petr Danecek	Added -f, -F options. Count and plot indels per cycle...	commit \| commitdiff \| tree \| snapshot
2012-05-17	Heng Li	change the default clevel to 1 for speed	commit \| commitdiff \| tree \| snapshot
2012-05-17	Heng Li	added bamshuf from htslib	commit \| commitdiff \| tree \| snapshot
2012-05-11	Heng Li	bugfix: bgzf-mt may write prematured output	commit \| commitdiff \| tree \| snapshot
2012-05-05	Heng Li	added length threshold	commit \| commitdiff \| tree \| snapshot
2012-05-03	Petr Danecek	Reverted to the previous behaviour, the unmapped reads...	commit \| commitdiff \| tree \| snapshot
2012-04-24	Petr Danecek	init_regions: check for non-matching sequence names	commit \| commitdiff \| tree \| snapshot
2012-04-23	Petr Danecek	Resolved merge conflict	commit \| commitdiff \| tree \| snapshot
2012-04-23	Petr Danecek	Indexed access can be now combined with target regions...	commit \| commitdiff \| tree \| snapshot
2012-04-17	Heng Li	r572: added "bedcov" command	commit \| commitdiff \| tree \| snapshot
2012-04-17	Heng Li	change getline() to mygetline()	commit \| commitdiff \| tree \| snapshot
2012-04-17	Heng Li	updated to the latest kseq	commit \| commitdiff \| tree \| snapshot
2012-04-12	Petr Danecek	Added check for out-of-bounds indels at the end of...	commit \| commitdiff \| tree \| snapshot
2012-04-12	Petr Danecek	On behalf of Bradford Powell: fixed typo in VCF header...	commit \| commitdiff \| tree \| snapshot
2012-04-04	Petr Danecek	Removed glibc dependency (getline)	commit \| commitdiff \| tree \| snapshot
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