Khalid Shakir 746a5e95f3 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. ... Updated HSP to use new padding arguments instead of flank intervals file, plus latest QC evals. IntervalUtils return unmodifiable lists so that utilities don't mutate the collections. Added a JavaCommandLineFunction.javaGCThreads option to test reducing java's automatic GC thread allocation based on num cpus. Added comma to list of characters to convert to underscores in GridEngine job names so that GE JSV doesn't choke on the -N values. JobRunInfo handles the null done times when jobs crash with strange errors.		2012-06-27 01:15:22 -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	CombineVariantsUnitTest was failing because the header repair was fixing the problem it wanted to detect	2012-06-26 17:32:42 -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