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2012-03-20	Heng Li	Merge branch 'master' into mt	commit \| commitdiff \| tree
2012-03-20	Heng Li	bugfix: downsampling not always working	commit \| commitdiff \| tree
2012-03-19	Heng Li	name sorting checkes READ1 and READ2	commit \| commitdiff \| tree
2012-03-19	Heng Li	sorting also considers strand	commit \| commitdiff \| tree
2012-03-18	Heng Li	change the default block size in sorting	commit \| commitdiff \| tree
2012-03-18	Heng Li	multi-threaded sorting	commit \| commitdiff \| tree
2012-03-18	Heng Li	added .gitignore	commit \| commitdiff \| tree
2012-03-18	Heng Li	added mt comression to merge	commit \| commitdiff \| tree
2012-03-18	Heng Li	updated the alphanum comparison function	commit \| commitdiff \| tree
2012-03-18	Heng Li	avoid wasting CPU time by the master thread	commit \| commitdiff \| tree
2012-03-18	Heng Li	use conditional variable	commit \| commitdiff \| tree
2012-03-18	Heng Li	bugfix in caching	commit \| commitdiff \| tree
2012-03-18	Heng Li	multi-threading working on toy examples	commit \| commitdiff \| tree
2012-03-18	Heng Li	preliminary implementation; not tested	commit \| commitdiff \| tree
2012-03-18	Heng Li	updated with the latest bgzf library	commit \| commitdiff \| tree
2012-03-09	Heng Li	On behalf of Petr: multi-allelic GT	commit \| commitdiff \| tree
2012-03-09	Heng Li	Removed SVN ChangeLog; merged my private github Log...	commit \| commitdiff \| tree
2012-03-09	Heng Li	doc for downsampling	commit \| commitdiff \| tree
2012-03-09	Heng Li	another example, used by g1k for QA	commit \| commitdiff \| tree
2012-03-09	Heng Li	Two auxilary Lua scripts	commit \| commitdiff \| tree
2012-03-09	Heng Li	Incoporated changes from Nils Homer.	commit \| commitdiff \| tree
2012-02-16	Heng Li	bugfix: wrong SP; missing DV in the VCF header	commit \| commitdiff \| tree
2012-02-08	Heng Li	changes from git	commit \| commitdiff \| tree
2011-09-28	Heng Li	unpadded output	commit \| commitdiff \| tree
2011-09-23	Heng Li	added the ace2sam converter	commit \| commitdiff \| tree
2011-09-23	Heng Li	converted padded SAM to unpadded SAM	commit \| commitdiff \| tree
2011-09-02	Heng Li	* Updated samtools to the latest	commit \| commitdiff \| tree
2011-08-17	Heng Li	* bugfix in index: large memory when a read pos is 1	commit \| commitdiff \| tree
2011-07-15	Heng Li	allow to set seed in view-subsampling	commit \| commitdiff \| tree
2011-07-15	Heng Li	subsampling read pairs	commit \| commitdiff \| tree
2011-07-13	Heng Li	support trio indels	commit \| commitdiff \| tree
2011-07-07	Heng Li	for WIN32 compatibility	commit \| commitdiff \| tree
2011-07-07	Heng Li	fixed a bug in bam_plcmd.c	commit \| commitdiff \| tree
2011-07-07	Heng Li	Release samtools-0.1.17	commit \| commitdiff \| tree
2011-06-15	Heng Li	fixed a bug caused by a recent patch	commit \| commitdiff \| tree
2011-06-03	Heng Li	* 0.1.16-dev (r969:252)	commit \| commitdiff \| tree
2011-04-22	Heng Li	Removed the pileup command	commit \| commitdiff \| tree
2011-04-22	Heng Li	Release samtools-0.1.16 (r963:234)	commit \| commitdiff \| tree
2011-04-21	Heng Li	fixed a bug in merge	commit \| commitdiff \| tree
2011-04-18	Heng Li	Added the support for the new SAM/BAM type "B"	commit \| commitdiff \| tree
2011-04-17	Heng Li	* fixed a bug in bedidx: input BED not sorted	commit \| commitdiff \| tree
2011-04-15	Heng Li	* Added Brent's method for frequency estimate	commit \| commitdiff \| tree
2011-04-10	Heng Li	Release samtools-0.1.15 (r949:203)	commit \| commitdiff \| tree
2011-04-08	Heng Li	* added bam_verbose global variable	commit \| commitdiff \| tree
2011-04-01	Heng Li	added quality filtering	commit \| commitdiff \| tree
2011-04-01	Heng Li	fixed a few typos in comments	commit \| commitdiff \| tree
2011-04-01	Heng Li	Added an example of using mpileup	commit \| commitdiff \| tree
2011-03-31	Heng Li	* synchronize bgzf in tabix and in samtools	commit \| commitdiff \| tree
2011-03-30	Heng Li	* added BED support to samtools view and mpileup and...	commit \| commitdiff \| tree
2011-03-22	Heng Li	Release samtools-0.1.14 (r933:170)	commit \| commitdiff \| tree
2011-03-18	Heng Li	forget to add this file	commit \| commitdiff \| tree
2011-03-18	Heng Li	* allow to change the compression level in BAM output	commit \| commitdiff \| tree
2011-03-18	Heng Li	export2sam.pl-2.3.1, provided by Chris Saunders from...	commit \| commitdiff \| tree
2011-03-08	Heng Li	added the haploid mode	commit \| commitdiff \| tree
2011-03-01	Heng Li	Release samtools-0.1.13 (r926:134)	commit \| commitdiff \| tree
2011-03-01	Heng Li	* optionally drop phase ambiguous reads	commit \| commitdiff \| tree
2011-02-28	Heng Li	minor changes to a heuristic rule	commit \| commitdiff \| tree
2011-02-28	Heng Li	* 0.1.12-r924:126	commit \| commitdiff \| tree
2011-02-28	Heng Li	* put version number in bam.h	commit \| commitdiff \| tree
2011-02-25	Heng Li	* change the order of PL/GL according to the latest...	commit \| commitdiff \| tree
2011-02-25	Heng Li	update the BCF spec	commit \| commitdiff \| tree
2011-02-25	Heng Li	added the phase command	commit \| commitdiff \| tree
2011-02-24	Heng Li	added "const" to bcf_p1_cal()	commit \| commitdiff \| tree
2011-02-24	Heng Li	more meaningful BAM truncation message	commit \| commitdiff \| tree
2011-02-24	Heng Li	* automatically fix errors in GL	commit \| commitdiff \| tree
2011-02-11	Heng Li	finished VCF->BCF conversion	commit \| commitdiff \| tree
2011-02-02	Heng Li	fixed a typo in the VCF header	commit \| commitdiff \| tree
2011-02-02	Heng Li	* fixed an out-of-boundary bug	commit \| commitdiff \| tree
2011-01-30	Heng Li	* avoid a segfault when network connect fails	commit \| commitdiff \| tree
2011-01-27	Heng Li	* fixed a rare memory issue in bam_md.c	commit \| commitdiff \| tree
2011-01-24	Heng Li	fixed two minor bugs in Fisher's exact test	commit \| commitdiff \| tree
2011-01-15	Heng Li	move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c	commit \| commitdiff \| tree
2011-01-06	Heng Li	* samtools-0.1.12-10 (r896)	commit \| commitdiff \| tree
2011-01-04	Heng Li	sorry. It is SP not ST	commit \| commitdiff \| tree
2011-01-04	Heng Li	added ST	commit \| commitdiff \| tree
2010-12-21	Heng Li	* samtools-0.1.12-9 (r891)	commit \| commitdiff \| tree
2010-12-15	Heng Li	* samtools-0.1.12-12 (r889)	commit \| commitdiff \| tree
2010-12-15	Heng Li	When -B is applied to mpileup, still use paired reads...	commit \| commitdiff \| tree
2010-12-15	Heng Li	* samtools-0.1.12-6 (r887)	commit \| commitdiff \| tree
2010-12-14	Heng Li	(Arguably) improved the indel caller a tiny bit for...	commit \| commitdiff \| tree
2010-12-13	Heng Li	* samtools-0.1.12-4 (r884)	commit \| commitdiff \| tree
2010-12-12	Heng Li	compute max SP and max GQ from sample genotypes	commit \| commitdiff \| tree
2010-12-10	Heng Li	drop bcf-fix.pl as it is redundant by the latest changes	commit \| commitdiff \| tree
2010-12-10	Heng Li	* fixed a minor issue in printing VCFs	commit \| commitdiff \| tree
2010-12-10	Heng Li	Make sure that the GT genotype field is the first	commit \| commitdiff \| tree
2010-12-08	Heng Li	* samtools-0.1.12-2 (r877)	commit \| commitdiff \| tree
2010-12-08	Heng Li	a spelling error..	commit \| commitdiff \| tree
2010-12-08	Heng Li	* samtools-0.1.12-1 (r873)	commit \| commitdiff \| tree
2010-12-07	Heng Li	fixed a bug in vcf2fq	commit \| commitdiff \| tree
2010-12-05	Heng Li	added a warning for the Windows version	commit \| commitdiff \| tree
2010-12-05	Heng Li	In ksprintf(), change "%lf" and "%lg" to "%f" and ...	commit \| commitdiff \| tree
2010-12-05	Heng Li	bring back the windows support	commit \| commitdiff \| tree
2010-12-05	Heng Li	Fixed a compiling error when knetfile is not used.	commit \| commitdiff \| tree
2010-12-04	Heng Li	vcf->fastq	commit \| commitdiff \| tree
2010-12-03	Heng Li	* remove "-f". Instead always compute consensus quality	commit \| commitdiff \| tree
2010-12-03	Heng Li	more informative error message	commit \| commitdiff \| tree
2010-12-02	Heng Li	Release samtools-0.1.12a	commit \| commitdiff \| tree
2010-12-02	Heng Li	a possible fix to DP4=0,0,0,0; have not tested, but...	commit \| commitdiff \| tree
2010-12-02	Heng Li	Release samtools-0.1.12	commit \| commitdiff \| tree
2010-12-02	Heng Li	* samtools-0.1.11-1 (r858)	commit \| commitdiff \| tree
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