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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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	BCF2 cleanup	2012-06-26 15:28:33 -04:00
test	BCF2 cleanup	2012-06-26 15:28:33 -04:00