gatk3的最后一个经典版本3.8

Mark DePristo b5fa848255 Fix GSA-515 Nanoscheduler GSA-573 -nt and -nct interact badly w.r.t. output ... -- See https://jira.broadinstitute.org/browse/GSA-573 -- Uses InheritedThreadLocal storage so that children threads created by the NanoScheduler see the parent stubs in the main thread. -- Added explicit integration test that checks that -nt 1, 2 and -nct 1, 2 give the same results for GLM BOTH with the UG over 1 MB.		2012-09-20 18:45:16 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table.	2012-09-20 14:14:34 -04:00
public	Fix GSA-515 Nanoscheduler GSA-573 -nt and -nct interact badly w.r.t. output	2012-09-20 18:45:16 -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