gatk3的最后一个经典版本3.8

Mark DePristo 91f3204534 VCF/BCF writers once again automatically write out no-call genotypes for samples in the VCFHeader but not in the VC itself ... -- Turns out this was consuming 30% of the UG runtime, and causing problems elsewhere. -- Removed addMissingSamples from VariantcontextUtils, and calls to it -- Updated VCF / BCF writers to automatically write out a diploid no call for missing samples -- Added unit tests for this behavior in VariantContextWritersUnitTest		2012-09-12 06:46:26 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Fix GSA-535: storing likelihoods in allele map was busted when running HaplotypeCaller, only the last likelihood of a haplotype was being stored, as opposed to the max likelihood of all haplotypes mapping to an allele	2012-09-11 11:01:26 -04:00
public	VCF/BCF writers once again automatically write out no-call genotypes for samples in the VCFHeader but not in the VC itself	2012-09-12 06:46:26 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.gitignore	a few more useful git ignores	2012-09-01 11:08:36 -04:00
build.xml	More memory for gatkdocs and extracthelp targets	2012-09-05 15:45:22 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00