Mark DePristo 7144154f53 VCFWriter and BCFWriter no longer allow missing samples in the VC compared to their header ... -- They now throw an error, as its really unsafe to write out ./. as a special case in the VCFWriter as occurred previously. -- Added convenience method in VariantContextUtils.addMissingSamples(vc, allSamples) that returns a complete VC where samples are given ./. Genotype objects -- This allows us to properly pass tests of creating / writing / reading VCFs and BCFs, which previously differed because the VC from the VCF would actually be different from its original VC -- Updated UG, UGEngine, GenotypeAndValidateWalker, CombineVariants, and VariantsToVCF to manage the master list of samples they are writing out and addMissingSamples via the VCU function		2012-06-28 10:06:06 -04:00
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R	Bugfix for R 2.15 not including reshape	2012-06-14 16:42:29 -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
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java	VCFWriter and BCFWriter no longer allow missing samples in the VC compared to their header	2012-06-28 10:06:06 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Temporary fake release directories for Bamboo testing purposes	2012-05-31 16:04:07 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Refactored parsing of Rod/IntervalBinding. Queue S/G now uses all interval arguments passed to CommandLineGATK QFunctions including support for BED/tribble types, XL, ISR, and padding.	2012-06-27 01:15:22 -04:00
testdata	Moved most testdata from public to private	2012-06-21 15:17:19 -04:00