Mark DePristo 41aba491c0 Critical bugfix for adapter clipping in HaplotypeCaller ... -- The previous code would adapter clip before reverting soft clips, so because we only clip the adapter when it's actually aligned (i.e., not in the soft clips) we were actually not removing bases in the adapter unless at least 1 bp of the adapter was aligned to the reference. Terrible. -- Removed the broken logic of determining whether a read adaptor is too long. -- Doesn't require isProperPairFlag to be set for a read to be adapter clipped -- Update integration tests for new adapter clipping code		2013-07-02 15:46:36 -04:00
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commandline	Fixed the logic of the @Output annotation and its interaction with 'required'.	2013-03-14 11:58:51 -04:00
gatk	Better GATK version and command line output	2013-06-20 11:19:13 -04:00
jna	Fix pipeline tests that were not respecting the pipeline test dry run setting	2013-06-28 15:27:17 -04:00
utils	Critical bugfix for adapter clipping in HaplotypeCaller	2013-07-02 15:46:36 -04:00
BaseTest.java	Fix pipeline tests that were not respecting the pipeline test dry run setting	2013-06-28 15:27:17 -04:00
ExampleToCopyUnitTest.java	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00
MD5DB.java	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
MD5Mismatch.java	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
StingTextReporter.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -05:00
WalkerTest.java	Reduce number of leftover temp files in GATK runs	2013-06-14 15:56:03 -04:00