Valentin Ruano-Rubio 08f92bb6f9 Added AnalyzeCovariates tool to generate BQSR assessment quality plots. ... Implemtation details: * Added tool class *.AnalyzeCovariates * Added convenient addAll method to Utils to be able to add elements of an array. * Added parameter comparison methods to RecalibrationArgumentCollection class in order to verify that multiple imput recalibration report are compatible and comparable. * Modified the BQSR.R script to handle up to 3 different recalibration tables (-BQSR, -before and -after) and removed some irrelevant arguments (or argument values) from the output. * Added an integration test class.		2013-06-19 14:38:02 -04:00
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R	Added AnalyzeCovariates tool to generate BQSR assessment quality plots.	2013-06-19 14:38:02 -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	Added AnalyzeCovariates tool to generate BQSR assessment quality plots.	2013-06-19 14:38:02 -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