Mark DePristo 010034a650 Optimization/bugfix for PerReadAlleleLikelihoodMap ... -- Add() call had a misplaced map.put call, so that we were always putting the result of get() back into the map, when what we really intended was to only put the value back in if the original get() resulted in a null and so initialized the result		2013-05-21 16:18:57 -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	Optimization/bugfix for PerReadAlleleLikelihoodMap	2013-05-21 16:18:57 -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