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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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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
..
datasources Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
downsampling Make downsampler classes themselves generic (instead of just the Downsampler interface) 2012-06-13 16:43:39 -04:00
executive Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
filters Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
iterators Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort. 2012-06-15 15:55:03 -04:00
refdata Minor bugfix -- now that the testfile is in our testdata regenerate the idx file as needed to pass tests 2012-06-26 15:28:32 -04:00
report Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
samples Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
traversals First pass of the asynchronous block loader. 2011-11-18 15:02:59 -05:00
walkers BCF2 cleanup 2012-06-26 15:28:33 -04:00
EngineFeaturesIntegrationTest.java Nearing final BCF commit 2012-06-14 16:42:32 -04:00
GenomeAnalysisEngineUnitTest.java Allow processing of empty intervals, but warn user when this case is encountered. 2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant. 2011-08-10 12:20:18 -04:00