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gatk-3.8/public/java/test/org/broadinstitute/sting
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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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commandline Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
gatk Final cleanup and unit testing for GATKRunReport 2013-02-02 15:06:56 -05:00
jna Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
utils -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
BaseTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ExampleToCopyUnitTest.java UnitTesting example for copying 2013-01-30 11:19:08 -05:00
MD5DB.java Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs 2013-01-30 16:42:23 -05:00
MD5Mismatch.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
StingTextReporter.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
WalkerTest.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00