Valentin Ruano-Rubio 1f8282633b Removed plots generation from the BaseRecalibration software ... Improved AnalyzeCovariates (AC) integration test. Renamed AC test files ending with .grp to .table Implementation: * Removed RECAL_PDF/CSV_FILE from RecalibrationArgumentCollection (RAC). Updated rest of the code accordingly. * Fixed BQSRIntegrationTest to work with new changes		2013-06-19 14:47:56 -04:00
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alignment	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
commandline	Optimization to method for getting values in ArgumentMatch	2013-04-04 23:30:47 -04:00
gatk	Merge pull request #295 from broadinstitute/dr_remove_PrintReads_ds_argument	2013-06-19 10:55:10 -07:00
jna	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
queue	change the default VCFs gatherer of the GATK (not just the UG)	2013-01-18 15:03:12 -05:00
tools	CatVariants accepts reference files ending in any standard extension	2013-06-19 11:10:36 -04:00
utils	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -04:00