Eric Banks 232afdcbea Added check in the MalformedReadFilter for reads without stored bases (i.e. that use '*'). ... * We now throw a User Error for such reads * User can override this to filter instead with --filter_bases_not_stored * Added appropriate unit test		2013-03-14 17:17:26 -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	Fixed bug in SelectVariants where maxIndelSize argument wasn't getting applied to deletions.	2013-03-13 15:11:34 -04:00
CommandLineGATKUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java	Increase timeout for a test in the EngineFeaturesIntegrationTest	2013-03-12 23:53:26 -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	Fix more tests that fail when run in parallel on the farm	2013-03-12 16:53:30 -04:00
WalkerManagerUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00