Yossi Farjoun de03f17be4 -Added Per-Sample Contamination Removal to UnifiedGenotyper: Added an @Advanced option to the StandardCallerArgumentCollection, a file which should ... contain two columns, Sample (String) and Fraction (Double) that form the Sample-Fraction map for the per-sample AlleleBiasedDownsampling. -Integration tests to UnifiedGenotyper (Using artificially contaminated BAMs created from a mixure of two broadly concented samples) were added -includes throwing an exception in HC if called using per-sample contamination file (not implemented); tested in a new integration test. -(Note: HaplotypeCaller already has "Flat" contamination--using the same fraction for all samples--what it doesn't have is _per-sample_ AlleleBiasedDownsampling, which is what has been added here to the UnifiedGenotyper. -New class: DefaultHashMap (a Defaulting HashMap...) and new function: loadContaminationFile (which reads a Sample-Fraction file and returns a map). -Unit tests to the new class and function are provided. -Added tests to see that malformed contamination files are found and that spaces and tabs are now read properly. -Merged the integration tests that pertain to biased downsampling, whether HaplotypeCaller or unifiedGenotyper, into a new IntegrationTest class.		2013-02-04 18:24:36 -05:00
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gatk	-Added Per-Sample Contamination Removal to UnifiedGenotyper: Added an @Advanced option to the StandardCallerArgumentCollection, a file which should	2013-02-04 18:24:36 -05:00
utils	Swap java Random generator for GATK one to ensure test determinism	2013-02-04 10:57:34 -05:00