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
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commandline	Fixed the logic of the @Output annotation and its interaction with 'required'.	2013-03-14 11:58:51 -04:00
gatk	Fixes to get accurate read counts for Read traversals	2013-05-21 15:24:07 -04:00
jna	Fix more tests that fail when run in parallel on the farm	2013-03-12 16:53:30 -04:00
utils	Subshard timeouts in the GATK	2013-05-15 07:00:39 -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