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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CNV	CombineVariants no longer adds PASS to unfiltered records	2013-05-20 16:53:51 -04:00
coverage	e# This is a combination of 2 commits.	2013-05-03 11:19:14 -04:00
qc	Fixes to get accurate read counts for Read traversals	2013-05-21 15:24:07 -04:00
readutils	Several improvements to ReadAdaptorTrimmer so that it can be incorporated into ancient DNA processing pipelines (for which it was developed):	2013-04-13 13:41:36 -04:00
variantutils	Fixed bug in SelectVariants where maxIndelSize argument wasn't getting applied to deletions.	2013-03-13 15:11:34 -04:00
BAQIntegrationTest.java	Update MD5s to reflect version number change in the BAM header	2013-02-01 13:51:31 -05:00