gatk3的最后一个经典版本3.8

Mark DePristo 7a462399ce Fix GSA-529: Fix RODs for parallel read walkers ... -- TraverseReadsNano modified to read in all input data before invoking maps, so the input to TraverseReadsNano is a MapData object holding the sam record, the ref context, and the refmetadatatracker. -- Update ValidateRODForReads to be tree reducible, using synchronized map and explicitly sort the output map from locations -> counts in onTraversalDone -- Expanded integration tests to test nt 1, 2, 4.		2012-08-30 19:41:49 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers	2012-08-30 10:15:10 -04:00
public	Fix GSA-529: Fix RODs for parallel read walkers	2012-08-30 19:41:49 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -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	Convert external.build.dir and external.dist.dir back to paths	2012-08-15 23:04:10 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00