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2012-12-12	Petr Danecek	mpileup: New --rf and --ff options for filtering reads	commit \| commitdiff \| tree
2012-12-12	Petr Danecek	bamcheck: New stats - the number of QC failed reads...	commit \| commitdiff \| tree
2012-12-12	Petr Danecek	bam2depth: Enabled reading the list of BAMs from a...	commit \| commitdiff \| tree
2012-12-11	Petr Danecek	ksort.h: declared __ks_insertsort_##name as static...	commit \| commitdiff \| tree
2012-12-03	Petr Danecek	bam_plcmd.c: more descriptive -b usage help message	commit \| commitdiff \| tree
2012-12-03	Petr Danecek	bam_plcmd.c: added sanity check in read_file_list,...	commit \| commitdiff \| tree
2012-12-03	Petr Danecek	bamcheck: New stats, number of pairs mapped to different...	commit \| commitdiff \| tree
2012-11-27	Petr Danecek	misc/Makefile, on behalf of ghuls: changed the order...	commit \| commitdiff \| tree
2012-11-27	Petr Danecek	bamcheck: max quality value increased to 255 to handle...	commit \| commitdiff \| tree
2012-11-22	Petr Danecek	bamcheck: Fixed a bug introduced by previous change...	commit \| commitdiff \| tree
2012-11-15	Petr Danecek	Merge remote branch 'remotes/pd3master/master' into...	commit \| commitdiff \| tree
2012-11-09	Petr Danecek	Drop empty bins from coverage distribution	commit \| commitdiff \| tree
2012-11-09	Petr Danecek	Changed default reflen; more informative error message...	commit \| commitdiff \| tree
2012-10-11	Petr Danecek	More user-friendly error output	commit \| commitdiff \| tree
2012-10-10	Petr Danecek	Complain when BAM cannot be open. Severe bug fixed...	commit \| commitdiff \| tree
2012-09-12	Petr Danecek	Merge remote branch 'remotes/pd3/master'	commit \| commitdiff \| tree
2012-09-05	Petr Danecek	Fix in insertion cycle calculation of rev reads	commit \| commitdiff \| tree
2012-09-05	Petr Danecek	GC-depth calculation now more robust to small GCD bin...	commit \| commitdiff \| tree
2012-09-04	Petr Danecek	New --GC-depth option to bamcheck. Take into account...	commit \| commitdiff \| tree
2012-08-02	Petr Danecek	Use int64_t to prevent count overflow in view -c; on...	commit \| commitdiff \| tree
2012-07-18	Petr Danecek	Fix in output of missing haploid genotypes	commit \| commitdiff \| tree
2012-07-05	Petr Danecek	Allow filtering by read group or sample name in bamcheck...	commit \| commitdiff \| tree
2012-07-05	Petr Danecek	VCF annotations with and without -m and more robust...	commit \| commitdiff \| tree
2012-07-03	Petr Danecek	Bug fixes	commit \| commitdiff \| tree
2012-07-02	Petr Danecek	Alternative model for multiallelic and rare-variant...	commit \| commitdiff \| tree
2012-06-27	Petr Danecek	New -p switch for increased sensititivy of indel-calling...	commit \| commitdiff \| tree
2012-06-21	Petr Danecek	Merge branch 'master' of github.com:samtools/samtools	commit \| commitdiff \| tree
2012-06-21	Petr Danecek	New -p option to start tview at desired position	commit \| commitdiff \| tree
2012-06-12	Petr Danecek	Merge remote branch 'rq/getopt_mac'	commit \| commitdiff \| tree
2012-06-07	Petr Danecek	New -s option for multisample BAMs: include only reads...	commit \| commitdiff \| tree
2012-05-30	Petr Danecek	Fixed errors introduced by the 8c15f916dabce475febdf508a9cc0...	commit \| commitdiff \| tree
2012-05-25	Petr Danecek	The -E switch to recalculate extended BAQ on the fly...	commit \| commitdiff \| tree
2012-05-25	Petr Danecek	Fix to prevent long stretches of Ns to be mistaken...	commit \| commitdiff \| tree
2012-05-18	Petr Danecek	Merge branch 'master' of github.com:samtools/samtools	commit \| commitdiff \| tree
2012-05-18	Petr Danecek	Added -f, -F options. Count and plot indels per cycle...	commit \| commitdiff \| tree
2012-05-03	Petr Danecek	Reverted to the previous behaviour, the unmapped reads...	commit \| commitdiff \| tree
2012-04-24	Petr Danecek	init_regions: check for non-matching sequence names	commit \| commitdiff \| tree
2012-04-12	Petr Danecek	Added check for out-of-bounds indels at the end of...	commit \| commitdiff \| tree
2012-04-12	Petr Danecek	On behalf of Bradford Powell: fixed typo in VCF header...	commit \| commitdiff \| tree
2012-04-04	Petr Danecek	Removed glibc dependency (getline)	commit \| commitdiff \| tree
2012-04-04	Petr Danecek	Merge remote branch 'main/master'	commit \| commitdiff \| tree
2012-04-02	Petr Danecek	Temporary fix to prevent segfault in kpa_glocal	commit \| commitdiff \| tree
2012-03-29	Petr Danecek	Compile cleanly from top-level Makefile. Check for...	commit \| commitdiff \| tree
2012-03-29	Petr Danecek	Compile cleanly from top-level Makefile. Check for...	commit \| commitdiff \| tree
2012-03-28	Petr Danecek	Added rule for bamcheck creation	commit \| commitdiff \| tree
2012-03-28	Petr Danecek	Added rule for bamcheck creation	commit \| commitdiff \| tree
2012-03-27	Petr Danecek	Initial release of bamcheck and plot-bamcheck	commit \| commitdiff \| tree
2012-03-27	Petr Danecek	Initial release of bamcheck and plot-bamcheck	commit \| commitdiff \| tree
2011-02-03	Petr Danecek	Prevent division by zero	commit \| commitdiff \| tree
2011-01-19	Petr Danecek	Skip sites with unknown ref	commit \| commitdiff \| tree
2011-01-04	Petr Danecek	Fixed a typo in read_samples	commit \| commitdiff \| tree
2010-12-14	Petr Danecek	Fixed the VCF header to pass validation	commit \| commitdiff \| tree
2010-11-02	Petr Danecek	Added -b option: read file names from a file	commit \| commitdiff \| tree
2010-10-05	Petr Danecek	Convert VCF output of "bcftools view -bgcv" to a valid...	commit \| commitdiff \| tree
2010-06-11	Petr Danecek	Initial release on behalf of Aylwyn Scally	commit \| commitdiff \| tree
2010-05-07	Petr Danecek	Added a note about the indels coordinates	commit \| commitdiff \| tree
2010-04-23	Petr Danecek	Added the possibility to print or not to print the...	commit \| commitdiff \| tree
2010-04-15	Petr Danecek	More descriptive message for space separated tags	commit \| commitdiff \| tree
2010-04-14	Petr Danecek	Speedup with -i, no need to query the reference all...	commit \| commitdiff \| tree
2010-03-15	Petr Danecek	Fixed the order of sequences in the header	commit \| commitdiff \| tree
2010-03-04	Petr Danecek	Added possibility to select indels only and fixed a...	commit \| commitdiff \| tree
2010-02-26	Petr Danecek	Improved efficiency of header parsing	commit \| commitdiff \| tree
2010-02-17	Petr Danecek	Fixed filtering of SNPs near indels. Added min indel...	commit \| commitdiff \| tree
2010-02-12	Petr Danecek	Print an error for pileups in simple format	commit \| commitdiff \| tree
2010-02-09	Petr Danecek	Added possibility to specify a custom column title...	commit \| commitdiff \| tree
2010-02-09	Petr Danecek	Added the -d option to limit maximum depth for indels.	commit \| commitdiff \| tree
2010-02-03	Petr Danecek	Added VCF header	commit \| commitdiff \| tree
2009-12-11	Petr Danecek	Fixed a bug in knet_seek	commit \| commitdiff \| tree
2009-12-11	Petr Danecek	Small fix in VCF format: dot for the empty INFO field	commit \| commitdiff \| tree
2009-12-11	Petr Danecek	Allow tabs in the CO header field	commit \| commitdiff \| tree
2009-10-24	Petr Danecek	Added sam_header_line_free call for sam_header_parse2	commit \| commitdiff \| tree
2009-10-23	Petr Danecek	Now possible to merge multiple HeaderDict dictionaries	commit \| commitdiff \| tree
2009-10-22	Petr Danecek	(no commit message)	commit \| commitdiff \| tree
2009-10-22	Petr Danecek	(no commit message)	commit \| commitdiff \| tree
2009-10-09	Petr Danecek	Added the sam2vcf.pl script.	commit \| commitdiff \| tree
2009-10-08	Petr Danecek	Removed the offending knet_seek message.	commit \| commitdiff \| tree
2009-10-06	Petr Danecek	Bug fix - faidx on RAZF compressed files now working.	commit \| commitdiff \| tree
2009-09-28	Petr Danecek	Changed the mode for newly created files to 0666. This...	commit \| commitdiff \| tree
2009-09-16	Petr Danecek	A bug fix, "samtools view" is now working again.	commit \| commitdiff \| tree

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