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
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java	Fixed nasty bug with defaulting to diploid no-call genotypes	2012-09-12 07:08:03 -04:00