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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R	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -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	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -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	Feature requested by Reich lab and Paavo lab in Leipzig for ancient DNA processing:	2013-06-17 13:21:09 -04:00
testdata	Somehow the index of exampleDBSNP.vcf was missing	2013-05-28 15:29:43 -04:00