gatk3的最后一个经典版本3.8

Ryan Poplin a36f4570c4 Adding two new output options in HaplotypeCaller for Menachem. The first controls the look ahead distance for turning consecutive SNPs into MNPs and the second outputs the full haplotype sequence for the active region instead of using Smith Waterman to find all the variants and output them in individual VCF records.		2012-03-30 14:09:38 -04:00
public	Deprecating AlignmentContext.getExtendedEventPileup(). At this point the only walkers left with any relaiance on extended events are Guillermo's pooled code (he'll update soon) and the Pileup walker. David, I'll leave that last one for you (it should be easy). We can now officially rip the extended event code from the engine.	2012-03-30 10:37:14 -04:00
settings	Rev. tribble to fix BED codec bug in tribble 51	2012-01-17 16:40:26 -05:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
LICENSE	Updated license year	2012-03-27 14:32:02 -04:00
build.xml	Bug fix to previous UnifiedGenotyperEngine refactoring, removed debug code	2012-03-25 10:20:21 -04:00
ivy.xml	S3 upload now directly creates the XML report in memory and puts that in S3	2012-01-29 15:14:58 -05:00