Mark DePristo 58c470a6c5 Rev'ing Tribble from 53 to 94 ... -- Other tribble contributors did major refactoring / simplification of tribble, which required some changes to GATK code -- Integrationtests pass without modification, though some very old index files (callable loci beds) were apparently corrupt and no longer tolerated by the newer tribble codebase		2012-05-03 07:31:47 -04:00
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R	Add warning message about ratios in variantQCreport, give ratio for MAF > 10%	2012-04-25 12:22:32 -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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Rev'ing Tribble from 53 to 94	2012-05-03 07:31:47 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Remove unnecessary and obscure usage of old R	2012-05-01 13:39:09 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Rev'ing Tribble from 53 to 94	2012-05-03 07:31:47 -04:00
testdata	continuing the BQSR triage...	2012-04-05 14:34:15 -04:00