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gatk-3.8/public/java/src/org/broadinstitute/sting/utils/collections
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Eric Banks 69b8173535 Replace uses of NestedHashMap with NestedIntegerArray. 
* Removed from codebase NestedHashMap since it is unused and untested.
 * Integration tests change because the BQSR CSV is now sorted automatically.
 * Resolves GSA-732
 		2013-02-27 14:03:39 -05:00
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DefaultHashMap.java -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
ExpandingArrayList.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
LoggingNestedIntegerArray.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
NestedIntegerArray.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Pair.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
PrimitivePair.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
RODMergingIterator.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00