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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R	Updating gsalib for R-3.0 compatibility	2013-05-18 12:43:38 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Fixes to get accurate read counts for Read traversals	2013-05-21 15:24:07 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
testdata	Revert changes to exampleFASTA.fasta.fai for now to get tests passing again	2013-05-02 12:59:20 -04:00