gatk-3.8

Author	SHA1	Message	Date
ebanks	647827b18c	Transitioned indel code to use GATK and Walkers git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@410 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-14 19:14:15 +00:00
asivache	f47a214f96	massive changes everywhere; lots of bugs fixed; methods moved around; computation and printout of overall stats added; now decides whether to accept or reject 'improvement'; writes alignments into two output sam files (unmodified reads/failed piles into one, realigned piles into the other); special treat for paranoids: writes third sam file with all the analyzed reads, unmodified git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@197 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-26 02:26:17 +00:00
asivache	40f45c2333	git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@184 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-25 05:48:10 +00:00