gatk3的最后一个经典版本3.8

Mauricio Carneiro edf08ca928 Updates to ReduceReads ... * Turn off the post-downsampler by default until new implementation. * optimized read clipping in consensus regions -- only clip once instead of every time the window slides. * extracted HeaderElement into it's own class. * moved RFA to archive * unified the context size of indels and mismatches		2012-06-08 14:57:34 -04:00
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
protected/java/src/org/broadinstitute/sting	build system overhaul	2012-05-17 15:16:29 -04:00
public	Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2012-06-08 13:54:48 -04:00
settings	Testing of BCF codec	2012-05-24 10:57:01 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	ant fasttest: for when you just can't wait	2012-06-01 15:17:18 -04:00
ivy.xml	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00