Eric Banks f172c349f6 Adding the functionality to enable users to input a file of VCFs for -V. ... To do this I have added a RodBindingCollection which can represent either a VCF or a file of VCFs. Note that e.g. SelectVariants allows a list of RodBindingCollections so that one can intermix VCFs and VCF lists. For VariantContext tags with a list, by default the tags for the -V argument are applied unless overridden by the individual line. In other words, any given line can have either one token (the file path) or two tokens (the new tags and the file path). For example: foo.vcf VCF,name=bar bar.vcf Note that a VCF list file name must end with '.list'. Added this functionality to CombineVariants, CombineReferenceCalculationVariants, and VariantRecalibrator.		2014-01-08 00:45:00 -05:00
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R	Something changed with the ggtitle syntax in the latest version of ggplot2.	2013-08-14 14:40:03 -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	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Adding the functionality to enable users to input a file of VCFs for -V.	2014-01-08 00:45:00 -05:00
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	Fixing the liftover script to not require strict VCF header validation.	2013-11-07 09:02:17 -05:00
scala	Added HC trio calls and NA12878 KB snapshot to resource bundle.	2013-12-07 22:08:34 -05:00
testdata	Walker to create a fastq file from an interval list	2013-06-29 11:24:16 -04:00