..
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
Command-line read filters are now applied before Walker default filters
2013-05-30 16:54:18 -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
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