Mark DePristo 74e153ff4a FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing ... -- Previously used hardcoded MAPQ > 20 && QUAL > 20 but now uses isUsableBase -- Updating MD5s as appropriate		2012-07-18 16:07:47 -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	FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing	2012-07-18 16:07:47 -04:00
EngineFeaturesIntegrationTest.java	Nearing final BCF commit	2012-06-14 16:42:32 -04:00
GenomeAnalysisEngineUnitTest.java	Refactored parsing of Rod/IntervalBinding. Queue S/G now uses all interval arguments passed to CommandLineGATK QFunctions including support for BED/tribble types, XL, ISR, and padding.	2012-06-27 01:15:22 -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