Eric Banks 881b2b50ab Optimized counting of filtered records by filter. ... Don't map class to counts in the ReadMetrics (necessitating 2 HashMap lookups for every increment). Instead, wrap the ReadFilters with a counting version and then set those counts only when updating global metrics.		2013-05-21 21:54:49 -04:00
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datasources	New ActiveRegionShardBalancer allows efficient NanoScheduling	2013-05-13 11:09:02 -04:00
downsampling	Setting the reduce reads count tag was all wrong in a previous commit; fixing.	2013-04-30 13:45:42 -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