David Roazen a7cb599945 Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage ... -Throw a UserException if a Locus or ActiveRegion walker is run with -dcov < 200, since low dcov values can result in problematic downsampling artifacts for locus-based traversals. -Read-based traversals continue to have no minimum for -dcov, since dcov for read traversals controls the number of reads per alignment start position, and even a dcov value of 1 might be safe/desirable in some circumstances. -Also reorganize the global downsampling defaults so that they are specified as annotations to the Walker, LocusWalker, and ActiveRegionWalker classes rather than as constants in the DownsamplingMethod class. -The default downsampling settings have not been changed: they are still -dcov 1000 for Locus and ActiveRegion walkers, and -dt NONE for all other walkers.		2013-05-29 12:07:12 -04:00
..
commandline	Fixed the logic of the @Output annotation and its interaction with 'required'.	2013-03-14 11:58:51 -04:00
gatk	Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage	2013-05-29 12:07:12 -04:00
jna	Fix more tests that fail when run in parallel on the farm	2013-03-12 16:53:30 -04:00
utils	Optimization for ActiveRegion.removeAll	2013-05-21 16:18:57 -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