Mark DePristo 5f5885ec78 Updating many MD5s to reflect correct fixed headers ... -- Previous bugfix ensures that header fixing is always on in the GATK by default, even after integration tests that failed and when through the VCFDiffableReader. Updating md5s to reflect this.		2012-06-26 15:28:34 -04:00
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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	Updating many MD5s to reflect correct fixed headers	2012-06-26 15:28:34 -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