gatk3的最后一个经典版本3.8

Ryan Poplin d1f2fe956f Changes to how active region triggering works around large insertions that manifest as high quality soft clips in read on one end of the insertion and low quality soft clips on the other end. The active region will now be large enough to capture the entire insertion. Need to somehow include unmapped reads with mapped mates to increase power for these events.		2012-04-06 13:17:41 -04:00
public	Adding function call in HaplotypeCaller right before the VariantContext gets written out to disk which partitions all the reads by which allele gave the read the highest likelihood. This will allow variants to be annotated by the refactored VariantAnnotator. Uninformative reads are mapped to Allele.NO_CALL	2012-04-06 00:22:52 -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