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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net/sf/samtools	Delete unused FastaSequenceIndexBuilder class and accompanying test	2013-05-01 01:02:01 -04:00
org/broadinstitute/sting	Fixes to get accurate read counts for Read traversals	2013-05-21 15:24:07 -04:00