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
..
commandline	Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"	2012-09-10 15:52:39 -04:00
gatk	Oops, missed this test before when updating md5s	2012-09-22 22:16:35 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Fixes GSA-515 Nanoscheduler GSA-577 -nt and -nct together appear to not close resources properly	2012-09-24 14:15:35 -04:00
BaseTest.java	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Renaming -cnt to -nct for consistency	2012-09-05 21:13:19 -04:00