hanna 41d57b7139 Massive cleanup of read filtering. ... - Eliminate reduncancy of filter application. - Track filter metrics per-shard to facitate per merging. - Flatten counting iterator hierarchy for easier debugging. - Rename Reads class to ReadProperties and track it outside of the Sting iterators. Note: because shards are currently tied so closely to reads and not the merged triplet of <reads,ref,RODs>, the metrics classes are managed by the SAMDataSource when they should be managed by something more general. For now, we're hacking the reads data source to manage the metrics; in the future, something more general should manage the metrics classes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4015 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-11 20:17:11 +00:00
..
alignment	Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath.	2010-04-01 17:17:16 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
oneoffprojects/walkers	fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric!	2010-06-29 21:38:55 +00:00
playground	adding tests for BTI in the ROD validation tests	2010-08-10 06:05:40 +00:00
utils	providing a way to specify how you'd like -BTI combined with your -L options; set BTIMR to either UNION (default) or INTERSECTION.	2010-08-09 14:00:52 +00:00
BaseTest.java	adding tests for BTI in the ROD validation tests	2010-08-10 06:05:40 +00:00
WalkerTest.java	fix for feature source in Tribble; we need to check that the record coming back isn't null. Also in the GATK added code to set the default logging level in integration tests to WARN, with the default level change they were spewing a bunch of text.	2010-08-10 02:57:23 +00:00