gatk3的最后一个经典版本3.8

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
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
protected/java	Moving ReduceReads into protected	2012-06-25 17:01:33 -04:00
public	VCFWriter and BCFWriter no longer allow missing samples in the VC compared to their header	2012-06-28 10:06:06 -04:00
settings	Rev tribble to 110. Log is:	2012-06-26 15:28:32 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	ant fasttest: for when you just can't wait	2012-06-01 15:17:18 -04:00
ivy.xml	JEXL update	2012-06-21 15:17:21 -04:00