Guillermo del Angel a971e7ab6d Several improvements to ReadAdaptorTrimmer so that it can be incorporated into ancient DNA processing pipelines (for which it was developed): ... -- Add pair cleaning feature. Reads in query-name sorted order are required and pairs need to appear consecutively, but if -cleanPairs option is set, a malformed pair where second read is missing is just skipped instead of erroring out. -- Add integration tests -- Move walker to public		2013-04-13 13:41:36 -04:00
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datasources	Remove auto-creation of fai/dict files for fasta references	2013-04-02 18:34:08 -04:00
downsampling	Add size() method to Downsampler interface	2013-04-08 15:48:13 -04:00
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	Make ActiveRegionTraversal robust to excessive coverage	2013-04-08 15:48:19 -04:00
walkers	Several improvements to ReadAdaptorTrimmer so that it can be incorporated into ancient DNA processing pipelines (for which it was developed):	2013-04-13 13:41:36 -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