Mark DePristo c1ac0e2760 BCF2 cleanup ... -- allowMissingVCFHeaders is now part of -U argument. If you want specifically unsafe VCF processing you need -U LENIENT_VCF_PROCESSING. Updated lots of files to use this -- LENIENT_VCF_PROCESSING disables on the fly VCF header cleanup. This is now implemented via a member variable, not a class variable, which I believe was changing the GATK behavior during integration tests, causing some files to fail that pass when run as a single test because the header reading behavior was changing depending on previous failures.		2012-06-26 15:28:33 -04:00
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net/sf	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
org/broadinstitute/sting	BCF2 cleanup	2012-06-26 15:28:33 -04:00