Mark DePristo cda8d944b7 Bugfixes for BCF with VQSR ... -- Old version converted doubles directly from strings. New version uses VariantContext getAttributeAsDouble() that looks at the values directly to determine how to convert from Object to Double (via Double.valueOf, (Double), or (Double)(Integer)). -- getAttributeAsDouble() is now smart in converting integers to doubles as needed -- Removed unnecessary logging info in BCF2Codec -- Added integration tests to ensure that VQSR works end-to-end with BCF2 using sites version of the file khalid sent to me -- Added vqsr.bcf_test.snps.unfiltered.bcf file for this integration test		2012-08-07 17:22:39 -04:00
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datasources	Add removeProgramRecords argument	2012-08-01 15:33:05 -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	RMDTrackBuilderUnitTest now uses private/testdata file to avoid filesystem race conditions	2012-07-25 22:05:04 -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	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
walkers	Bugfixes for BCF with VQSR	2012-08-07 17:22:39 -04:00
CommandLineGATKUnitTest.java	Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us.	2012-07-18 21:48:58 -04:00
EngineFeaturesIntegrationTest.java	Sorting out HMS error handling (fingers crossed)	2012-07-25 23:13:12 -04:00
GenomeAnalysisEngineUnitTest.java	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
WalkerManagerUnitTest.java	Fixing walker unit test with the new naming convention	2012-07-20 17:50:29 -04:00