Eric Banks 881b2b50ab Optimized counting of filtered records by filter. ... Don't map class to counts in the ReadMetrics (necessitating 2 HashMap lookups for every increment). Instead, wrap the ReadFilters with a counting version and then set those counts only when updating global metrics.		2013-05-21 21:54:49 -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	Optimized counting of filtered records by filter.	2013-05-21 21:54:49 -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