Mark DePristo 7b22467148 Bugfix: defaultBaseQualities actually works now ... -- It was being applied in the wrong order (after the first call to the underlying MalformedReadFilter) so if your first read was malformed you'd blow up there instead of being fixed properly. Added integration tests to ensure this continues to work. -- [delivers #49538319]		2013-06-17 14:37:27 -04:00
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datasources	Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP	2013-06-10 16:20:31 -04:00
downsampling	Exclude reduced reads from elimination during downsampling	2013-06-11 16:16:26 -04:00
executive	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	This commit addresses JIRA issue GSA-948: Prevent users from doing the wrong thing with RNA-Seq data and the GATK.	2013-06-10 10:44:42 -04:00
iterators	Refactor LIBS into utils.locusiterator before refactoring	2013-01-11 15:17:16 -05:00
refdata	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
report	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
samples	Trivial update to ceutrio.ped file to make it really the CEU trio sample names	2013-05-14 17:08:13 -04:00
traversals	Exclude reduced reads from elimination during downsampling	2013-06-11 16:16:26 -04:00
walkers	Fixes to get accurate read counts for Read traversals	2013-05-21 15:24:07 -04:00
CommandLineGATKUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java	Bugfix: defaultBaseQualities actually works now	2013-06-17 14:37:27 -04:00
GenomeAnalysisEngineUnitTest.java	Added the functionality to impose a relative ordering on ReadTransformers in the GATK engine.	2013-03-06 12:38:59 -05:00
MaxRuntimeIntegrationTest.java	Subshard timeouts in the GATK	2013-05-15 07:00:39 -04:00
ReadMetricsUnitTest.java	Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP	2013-06-10 16:20:31 -04:00
WalkerManagerUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00