depristo b8d6a95e7a Preliminary commit of new VCFCombine, soon to be called CombineVariants (next commit) that support merging any number of VCF files via a general VC merge routine that support prioritization and merging of samples! It's now possible to merge the pilot1/2/3 call sets into a single (monster) VCF taking genotypes from pilot2, then pilot3, then pilot1 as needed. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3690 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-30 20:13:03 +00:00
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NameAwareCodec.java	Preliminary commit of new VCFCombine, soon to be called CombineVariants (next commit) that support merging any number of VCF files via a general VC merge routine that support prioritization and merging of samples! It's now possible to merge the pilot1/2/3 call sets into a single (monster) VCF taking genotypes from pilot2, then pilot3, then pilot1 as needed.	2010-06-30 20:13:03 +00:00
VCFCodec.java	moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output	2010-06-25 18:20:06 +00:00
VCFFilterHeaderLine.java	moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output	2010-06-25 18:20:06 +00:00
VCFFormatHeaderLine.java	Fixes to better deal with the "Type" and "Number" field in the INFO and FORMAT header lines in VCF4.0. We now record these fields and provide appropriate conversions. This is the first version that passes fully the VCF validator.	2010-06-29 16:43:00 +00:00
VCFGenotypeEncoding.java	1) Initial complete version of VCF4 writer. There are still issues (see below) but at least this version is fully functional. It incorporates getting rid of intermediate VCFRecord so we now operate from VariantContext objects directly to VCF 4.0 output.	2010-06-28 23:54:38 +00:00
VCFGenotypeRecord.java	More necessary fixes for VCF4.0 - now results look more sensible in realistic, bigger VCF files produced by say Dindel and not just the small test VCF:	2010-06-30 02:59:30 +00:00
VCFHeader.java	moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output	2010-06-25 18:20:06 +00:00
VCFHeaderLine.java	moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output	2010-06-25 18:20:06 +00:00
VCFHeaderLineTranslator.java	moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output	2010-06-25 18:20:06 +00:00
VCFHeaderVersion.java	moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output	2010-06-25 18:20:06 +00:00
VCFInfoHeaderLine.java	moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output	2010-06-25 18:20:06 +00:00
VCFReaderUtils.java	moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output	2010-06-25 18:20:06 +00:00
VCFRecord.java	moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output	2010-06-25 18:20:06 +00:00