Mark DePristo c8ed0bfc4c Edge case fixes for BCF2 ... --handle entirely missing GT in a sample in decodeGenotypeAlleles --Create MAX_ALLELES_IN_GENOTYPES constant in BCF2Utils, and extracted its use inline from the code -- Generalized genotype writing code to handle ploidy != 2 and variable ploidy among samples -- Remove special case inline treatment of case where all samples have no GT field values, and moved this into calcVCFGenotypeKeys -- Removed restriction on getPloidy requiring ploidy > 1. It's logically find to return 0 for a no called sample -- getMaxPloidy() in VC that does what it says -- Support for padding / depadding of generic genotype fields		2012-05-24 10:57:06 -04:00
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net/sf	Fix serious engine bug that could cause reads to be dropped under certain circumstances	2012-02-13 16:25:21 -05:00
org/broadinstitute/sting	Edge case fixes for BCF2	2012-05-24 10:57:06 -04:00