gatk3的最后一个经典版本3.8

Mark DePristo a6b3497eac Fixes GSA-515 Nanoscheduler GSA-577 -nt and -nct together appear to not close resources properly ... -- Fixes monster bug in the way that traversal engines interacted with the NanoScheduler via the output tracker. -- ThreadLocalOutputTracker is now a ThreadBasedOutputTracker that associates via a map from a master thread -> the storage map. Lookups occur by walking through threads in the same thread group, not just the thread itself (TBD -- should have a map from ThreadGroup instead) -- Removed unnecessary debug statement in GenomeLocParser -- nt and nct officially work together now		2012-09-24 14:15:35 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	RR bug: we were adding synthetic reads from the header only before the variant region, which meant that reads that overlap the variant region but that weren't used for the consensus (because e.g. of low base quality for the spanning base) were never being used at all. Instead, add synthetic reads from before and spanning the variant region.	2012-09-24 13:29:37 -04:00
public	Fixes GSA-515 Nanoscheduler GSA-577 -nt and -nct together appear to not close resources properly	2012-09-24 14:15:35 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.gitignore	a few more useful git ignores	2012-09-01 11:08:36 -04:00
build.xml	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00