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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Mark DePristo 8d9b0f1bd5 Restructure ActivityProfiler into root class ActivityProfile and derived class BandPassActivityProfile 
-- Required before I jump in an redo the entire activity profile so it's can be run imcrementally
-- This restructuring makes the differences between the two functionalities clearer, as almost all of the functionality is in the base class. The only functionality provided by the BandPassActivityProfile is isolated to a finalizeProfile function overloaded from the base class.
-- Renamed ActivityProfileResult to ActivityProfileState, as this is a clearer indication of its actual functionality.  Almost all of the misc. walker changes are due to this name update
-- Code cleanup and docs for TraverseActiveRegions
-- Expanded unit tests for ActivityProfile and ActivityProfileState
 		2013-01-23 13:45:21 -05:00
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R Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
activeregion Restructure ActivityProfiler into root class ActivityProfile and derived class BandPassActivityProfile 2013-01-23 13:45:21 -05:00
baq Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
clipping Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
codecs/hapmap Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
collections Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
crypt Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fasta Added tests for changing IUPAC bases to Ns, for failing on bad ref bases, and for the HaplotypeCaller not failing when running over a region with an IUPAC base. 2013-01-16 14:55:33 -05:00
fragments Updating to latest google caliper code 2013-01-11 15:17:16 -05:00
interval Re-committing the following changes from Dec 18: 2013-01-16 12:43:15 -05:00
io Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
locusiterator Last manual license update (hopefully) 2013-01-18 16:13:07 -05:00
nanoScheduler Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
pileup Last manual license update (hopefully) 2013-01-18 16:13:07 -05:00
progressmeter Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
recalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
report Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
runtime Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
sam Last manual license update (hopefully) 2013-01-18 16:13:07 -05:00
text Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
threading Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
BitSetUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocParserUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocSortedSetUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
HaplotypeUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
LegacyReservoirDownsamplerUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MWUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MathUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MedianUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
PathUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
QualityUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
SimpleTimerUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
UtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00