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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java	Adding the functionality to enable users to input a file of VCFs for -V.	2014-01-08 00:45:00 -05:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00