gatk3的最后一个经典版本3.8

Mark DePristo bfbf1686cd Fixed nasty bug with defaulting to diploid no-call genotypes ... -- For the pooled caller we were writing diploid no-calls even when other samples were haploid. Changed maxPloidy function to return a defaultPloidy, rather than 0, in the case where all samples are missing. -- VCF/BCF Writers now create missing genotypes with the ploidy of other samples, or 2 if none are available at all. -- Updating integration tests for general ploidy, as previously we wrote ./. even when other calls were 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/1/1/1/1/1, but now we write ./././././././././././././././././././././././. (ugly but correct)		2012-09-12 07:08:03 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Fixed nasty bug with defaulting to diploid no-call genotypes	2012-09-12 07:08:03 -04:00
public	Fixed nasty bug with defaulting to diploid no-call genotypes	2012-09-12 07:08:03 -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