gatk3的最后一个经典版本3.8

Mauricio Carneiro ee9a56ad27 Fix subtle bug in the ReduceReads stash reported by Adam ... * The tailSet generated every time we flush the reads stash is still being affected by subsequent clears because it is just a pointer to the parent element in the original TreeSet. This is dangerous, and there is a weird condition where the clear will affects it. * Fix by creating a new set, given the tailSet instead of trying to do magic with just the pointer.		2012-02-23 18:35:25 -05:00
public	Fix subtle bug in the ReduceReads stash reported by Adam	2012-02-23 18:35:25 -05:00
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	One last test...	2011-06-28 19:18:17 -04:00
build.xml	Merged bug fix from Stable into Unstable	2012-01-24 15:19:29 -05:00
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