gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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
..
datasources Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage 2013-05-29 12:07:12 -04:00
downsampling Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage 2013-05-29 12:07:12 -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 Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -04:00
report Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
samples Trivial update to ceutrio.ped file to make it really the CEU trio sample names 2013-05-14 17:08:13 -04:00
traversals Count Reads should use a Long instead of an Integer for counts to prevent overflows. Added unit test. 2013-05-21 15:23:51 -04:00
walkers Fixes to get accurate read counts for Read traversals 2013-05-21 15:24:07 -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 Subshard timeouts in the GATK 2013-05-15 07:00:39 -04:00
ReadMetricsUnitTest.java Optimized counting of filtered records by filter. 2013-05-21 21:54:49 -04:00
WalkerManagerUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00