Mark DePristo 5894d045cb Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests ... -- This version of BCF should actually work properly for most files, assuming headers are properly defined. -- Lots of bug fixes to BCF2 codec -- Genotype getPhredScaledQual is now an int, returning -1 if there's no QUAL. NOTE THIS SEMANTICS change -- Equals() method for GenotypeLikelihoods, using PLs. -- VCFCodec now longer adds empty bindings to missing input field values. NOTE THIS CHANGE -- VCs can be marked as fully decoded, so that when fullyDecode() is called it returns itself, instead of doing the decoding work. The BCF2 codec now makes VCs marked as fully decoded -- stringToBytes returns empty list for null or "" string in BCF2Encoder -- Proper handling of genotype ordering in BCF2 reader / writer -- Removed the crazy slow noDups and sameSamples tests that were slowing down unit and integration tests totally unnecessarily -- Many failing MD5s now due to double -> int change in GQ, will update later		2012-05-27 11:17:17 -04:00
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net/sf	Merged bug fix from Stable into Unstable	2012-02-13 16:37:11 -05:00
org/broadinstitute/sting	Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests	2012-05-27 11:17:17 -04:00