Mark DePristo b16de45ce4 Command-line read filters are now applied before Walker default filters ... -- This allows us to use -rf ReassignMappingQuality to reassign mapping qualities to 60 *before* the BQSR filters them out with MappingQualityUnassignedFilter. -- delivers #50222251		2013-05-30 16:54:18 -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	Command-line read filters are now applied before Walker default filters	2013-05-30 16:54:18 -04:00
jna	Fix more tests that fail when run in parallel on the farm	2013-03-12 16:53:30 -04:00
utils	Create a new normalDistributionLog10 function that is unit tested for use in the VQSR.	2013-05-30 16:00:08 -04:00
BaseTest.java	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00
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	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00