gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
Eric Banks 20c7a89030 Fixes to get accurate read counts for Read traversals
1. Don't clone the dataSource's metrics object (because then the engine won't continue to get updated counts)
 2. Use the dataSource's metrics object in the CountingFilteringIterator and not the first shard's object!
 3. Synchronize ReadMetrics.incrementMetrics to prevent race conditions.

Also:
 * Make sure users realize that the read counts are approximate in the print outs.
 * Removed a lot of unused cruft from the metrics object while I was in there.
 * Added test to make sure that the ReadMetrics read count does not overflow ints.
 * Added unit tests for traversal metrics (reads, loci, and active region traversals); these test counts of reads and records.
2013-05-21 15:24:07 -04:00
..
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 Fixes to get accurate read counts for Read traversals 2013-05-21 15:24:07 -04:00
WalkerManagerUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00