Mauricio Carneiro eb33da6820 Added support to reduce reads to Callable Loci ... -- added calls to representativeCount() of the pileup instead of using ++ -- renamed CallableLoci integration test -- added integration test for reduce read support on callable loci		2013-03-21 15:53:04 -04:00
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datasources	Fixed the add functionality of GenomeLocSortedSet.	2013-02-28 23:31:00 -05:00
downsampling	- Changed loadContaminationFile file parser to delimit by tab only. This allows spaces in sampleIDs, which apparently are allowed.	2013-03-07 13:04:24 -05:00
executive	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Added check in the MalformedReadFilter for reads without stored bases (i.e. that use '*').	2013-03-14 17:17:26 -04:00
iterators	Refactor LIBS into utils.locusiterator before refactoring	2013-01-11 15:17:16 -05:00
refdata	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
report	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
samples	Updating TestNG to the latest version	2013-02-22 09:40:23 -05:00
traversals	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -05:00
walkers	Added support to reduce reads to Callable Loci	2013-03-21 15:53:04 -04:00
CommandLineGATKUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java	Further tweaking of test timeouts	2013-03-15 14:49:21 -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	Bump timeout for MaxRuntimeIntegrationTest	2013-03-17 16:17:29 -04:00
WalkerManagerUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00