Mark DePristo 7c5cdb51c2 UnitTests for ActivityProfile and minor ART cleanup ... -- TODO for ryan -- there are bugs in ActivityProfile code that I cannot fix right now :-( -- UnitTesting framework for ActivityProfile -- needs to be expanded -- Minor helper functions for ActiveRegion to help with unit tests		2012-03-14 17:26:37 -04:00
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TraversalEngine.java	Start printing traversal stats after 30 seconds. I can't stand waiting 2 minutes.	2011-12-22 15:40:59 -05:00
TraverseActiveRegions.java	UnitTests for ActivityProfile and minor ART cleanup	2012-03-14 17:26:37 -04:00
TraverseDuplicates.java	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
TraverseLoci.java	Documentation request by Eric. At each stage of the GATK where filtering occurs, added documentation suggesting the goal of the filtering along with examples of suggested inputs and outputs.	2012-02-09 11:24:52 -05:00
TraverseReadPairs.java	Walker.isDone() aborts execution early	2011-08-23 16:53:06 -04:00
TraverseReads.java	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
package-info.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00