git.donarmstrong.com Git - samtools.git/history

]> git.donarmstrong.com Git - samtools.git/history - bam_plcmd.c

2012-10-10	Petr Danecek	Complain when BAM cannot be open. Severe bug fixed...	blob \| commitdiff \| raw
2012-09-12	Petr Danecek	Merge remote branch 'remotes/pd3/master'	blob \| commitdiff \| raw \| diff to current
2012-06-27	Petr Danecek	New -p switch for increased sensititivy of indel-callin...	blob \| commitdiff \| raw \| diff to current
2012-05-25	Petr Danecek	The -E switch to recalculate extended BAQ on the fly...	blob \| commitdiff \| raw \| diff to current
2012-02-08	Heng Li	changes from git	blob \| commitdiff \| raw \| diff to current
2011-07-07	Heng Li	fixed a bug in bam_plcmd.c	blob \| commitdiff \| raw \| diff to current
2011-07-07	Heng Li	Release samtools-0.1.17	blob \| commitdiff \| raw \| diff to current
2011-06-03	Heng Li	* 0.1.16-dev (r969:252)	blob \| commitdiff \| raw \| diff to current
2011-04-22	Heng Li	Removed the pileup command	blob \| commitdiff \| raw \| diff to current
2011-04-10	Heng Li	Release samtools-0.1.15 (r949:203)	blob \| commitdiff \| raw \| diff to current
2011-04-08	Heng Li	* added bam_verbose global variable	blob \| commitdiff \| raw \| diff to current
2011-03-30	Heng Li	* added BED support to samtools view and mpileup and...	blob \| commitdiff \| raw \| diff to current
2011-03-22	Heng Li	Release samtools-0.1.14 (r933:170)	blob \| commitdiff \| raw \| diff to current
2011-03-18	Heng Li	* allow to change the compression level in BAM output	blob \| commitdiff \| raw \| diff to current
2011-02-28	Heng Li	* put version number in bam.h	blob \| commitdiff \| raw \| diff to current
2011-02-25	Heng Li	added the phase command	blob \| commitdiff \| raw \| diff to current
2011-01-06	Heng Li	* samtools-0.1.12-10 (r896)	blob \| commitdiff \| raw \| diff to current
2010-12-15	Heng Li	When -B is applied to mpileup, still use paired reads...	blob \| commitdiff \| raw \| diff to current
2010-12-15	Heng Li	* samtools-0.1.12-6 (r887)	blob \| commitdiff \| raw \| diff to current
2010-12-08	Heng Li	* samtools-0.1.12-2 (r877)	blob \| commitdiff \| raw \| diff to current
2010-12-08	Heng Li	a spelling error..	blob \| commitdiff \| raw \| diff to current
2010-12-08	Heng Li	* samtools-0.1.12-1 (r873)	blob \| commitdiff \| raw \| diff to current
2010-12-02	Heng Li	* samtools-0.1.11-1 (r858)	blob \| commitdiff \| raw \| diff to current
2010-11-19	Heng Li	* samtools-0.1.10-4 (r840)	blob \| commitdiff \| raw \| diff to current
2010-11-18	Heng Li	* samtools-0.1.10 (r831)	blob \| commitdiff \| raw \| diff to current
2010-11-16	Heng Li	* samtools-0.1.9-17 (r824)	blob \| commitdiff \| raw \| diff to current
2010-11-11	Heng Li	* samtools-0.1.9-9 (r810)	blob \| commitdiff \| raw \| diff to current
2010-11-10	Heng Li	* samtools-0.1.9-8 (r809)	blob \| commitdiff \| raw \| diff to current
2010-11-10	Heng Li	* samtools-0.1.9-8 (r807)	blob \| commitdiff \| raw \| diff to current
2010-11-08	Heng Li	* samtools-0.1.9-2 (r797)	blob \| commitdiff \| raw \| diff to current
2010-11-08	Heng Li	indel calling is apparently working, but more informati...	blob \| commitdiff \| raw \| diff to current
2010-11-08	Heng Li	prepare for the indel caller. It is not ready yet.	blob \| commitdiff \| raw \| diff to current
2010-11-05	Heng Li	Revert to r790. The recent changes are not good...	blob \| commitdiff \| raw \| diff to current
2010-11-05	Heng Li	* this revision is UNSTABLE	blob \| commitdiff \| raw \| diff to current
2010-11-05	Heng Li	for backup. no effective changes	blob \| commitdiff \| raw \| diff to current
2010-11-02	Petr Danecek	Added -b option: read file names from a file	blob \| commitdiff \| raw \| diff to current
2010-10-30	Heng Li	* samtools-0.1.9-2 (r787)	blob \| commitdiff \| raw \| diff to current
2010-10-29	Heng Li	* samtools-0.1.9-1 (r786)	blob \| commitdiff \| raw \| diff to current
2010-10-29	Heng Li	Optionally output "DP", the individual read depth	blob \| commitdiff \| raw \| diff to current
2010-10-27	Heng Li	fixed a silly bug in pileup	blob \| commitdiff \| raw \| diff to current
2010-10-27	Heng Li	* samtools-0.1.8-22 (r781)	blob \| commitdiff \| raw \| diff to current
2010-10-27	Heng Li	* samtools-0.1.8-21 (r780)	blob \| commitdiff \| raw \| diff to current
2010-10-27	Heng Li	improve pileup a little bit	blob \| commitdiff \| raw \| diff to current
2010-10-27	Heng Li	* samtools-0.1.8-20 (r778)	blob \| commitdiff \| raw \| diff to current
2010-10-26	Heng Li	* samtools-0.1.8-19 (r777)	blob \| commitdiff \| raw \| diff to current
2010-10-03	Heng Li	* samtools-0.1.8-18 (r763)	blob \| commitdiff \| raw \| diff to current
2010-09-28	Heng Li	prob_realn() seems working!	blob \| commitdiff \| raw \| diff to current
2010-09-27	Heng Li	...	blob \| commitdiff \| raw \| diff to current
2010-09-16	Heng Li	* samtools-0.1.8-14 (r727)	blob \| commitdiff \| raw \| diff to current
2010-09-16	Heng Li	* added varFilter to vcfutils.pl	blob \| commitdiff \| raw \| diff to current
2010-09-15	Heng Li	fixed a bug in realignment	blob \| commitdiff \| raw \| diff to current
2010-09-14	Heng Li	minor changes. It is BUGGY now!	blob \| commitdiff \| raw \| diff to current
2010-08-23	Heng Li	change the default correlation coefficient	blob \| commitdiff \| raw \| diff to current
2010-08-23	Heng Li	* samtools-0.1.8-12 (r692)	blob \| commitdiff \| raw \| diff to current
2010-08-23	Heng Li	remove VCF output in mpileup	blob \| commitdiff \| raw \| diff to current
2010-08-20	Heng Li	added revised MAQ error model	blob \| commitdiff \| raw \| diff to current
2010-08-05	Heng Li	* the code base is stablized again.	blob \| commitdiff \| raw \| diff to current
2010-08-04	Heng Li	* allow to set min base q	blob \| commitdiff \| raw \| diff to current
2010-08-02	Heng Li	Generate binary VCF	blob \| commitdiff \| raw \| diff to current
2010-07-28	Heng Li	supposedly this is THE correct implementation, but...	blob \| commitdiff \| raw \| diff to current
2010-07-26	Heng Li	* samtools-0.1.8-7 (r639)	blob \| commitdiff \| raw \| diff to current
2010-07-25	Heng Li	* samtools-0.1.8-6 (r638)	blob \| commitdiff \| raw \| diff to current
2010-07-24	Heng Li	minor changes	blob \| commitdiff \| raw \| diff to current
2010-07-24	Heng Li	minor tweaks	blob \| commitdiff \| raw \| diff to current
2010-07-24	Heng Li	posterior expectation FINALLY working. I am so tired...	blob \| commitdiff \| raw \| diff to current
2010-07-23	Heng Li	another minor fix to mpileup	blob \| commitdiff \| raw \| diff to current
2010-07-23	Heng Li	added the format column	blob \| commitdiff \| raw \| diff to current
2010-07-23	Heng Li	added an alternative prior	blob \| commitdiff \| raw \| diff to current
2010-07-23	Heng Li	calculate posterior allele frequency	blob \| commitdiff \| raw \| diff to current
2010-07-23	Heng Li	* samtools-0.1.8-3 (r627)	blob \| commitdiff \| raw \| diff to current
2010-07-22	Heng Li	* preliminary multisample SNP caller.	blob \| commitdiff \| raw \| diff to current
2010-07-14	Heng Li	* samtools-0.1.8-2 (r617)	blob \| commitdiff \| raw \| diff to current
2010-07-14	Heng Li	* added mutli-sample framework. It is not working...	blob \| commitdiff \| raw \| diff to current
2010-07-13	Heng Li	* samtools-0.1.8-1 (r615)	blob \| commitdiff \| raw \| diff to current
2010-07-12	Heng Li	Release samtools-0.1.8	blob \| commitdiff \| raw \| diff to current
2010-07-09	Heng Li	change the command line option of pileup	blob \| commitdiff \| raw \| diff to current
2010-07-09	Heng Li	* make tview more friendly	blob \| commitdiff \| raw \| diff to current
2010-07-08	Heng Li	* samtools-0.1.7-r607	blob \| commitdiff \| raw \| diff to current
2010-06-12	Heng Li	rename iterf as iter	blob \| commitdiff \| raw \| diff to current
2010-06-12	Heng Li	* samtools-0.1.7-15 (r592)	blob \| commitdiff \| raw \| diff to current
2010-06-12	Heng Li	* samtools-0.1.7-14 (r591)	blob \| commitdiff \| raw \| diff to current
2010-02-11	Heng Li	added a hidden option in pileup to output the base...	blob \| commitdiff \| raw \| diff to current
2010-02-09	Petr Danecek	Added the -d option to limit maximum depth for indels.	blob \| commitdiff \| raw \| diff to current
2010-02-01	Heng Li	* samtools-0.1.7-6	blob \| commitdiff \| raw \| diff to current
2009-12-14	Heng Li	* samtools-0.1.7-5 (r528)	blob \| commitdiff \| raw \| diff to current
2009-12-01	Heng Li	* samtools-0.1.7-2 (r520)	blob \| commitdiff \| raw \| diff to current
2009-11-06	Heng Li	* samtools-0.1.6-22 (r509)	blob \| commitdiff \| raw \| diff to current
2009-11-06	Heng Li	* samtools-0.1.6-21 (r508)	blob \| commitdiff \| raw \| diff to current
2009-10-18	Heng Li	* samtools-0.1.6-13 (r479)	blob \| commitdiff \| raw \| diff to current
2009-07-31	Heng Li	* samtools-0.1.5-18 (r423)	blob \| commitdiff \| raw \| diff to current
2009-07-30	Heng Li	* samtools-0.1.5-16 (r421)	blob \| commitdiff \| raw \| diff to current
2009-07-02	Heng Li	* samtools-0.1.4-22 (r369)	blob \| commitdiff \| raw \| diff to current
2009-06-16	Heng Li	* samtools-0.1.4-13 (r350)	blob \| commitdiff \| raw \| diff to current
2009-06-13	Heng Li	* samtools-0.1.4-12 (r347)	blob \| commitdiff \| raw \| diff to current
2009-06-13	Heng Li	* samtools-0.1.4-10 (r341)	blob \| commitdiff \| raw \| diff to current
2009-06-10	Heng Li	* samtools-0.1.4-3 (r324)	blob \| commitdiff \| raw \| diff to current
2009-06-08	Heng Li	* samtools-0.1.4-2 (r316)	blob \| commitdiff \| raw \| diff to current
2009-05-21	Heng Li	Release samtools-0.1.4	blob \| commitdiff \| raw \| diff to current
2009-05-05	Heng Li	* samtools-0.1.3-13 (r260)	blob \| commitdiff \| raw \| diff to current
2009-05-05	Heng Li	* samtools-0.1.3-12 (r259)	blob \| commitdiff \| raw \| diff to current
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