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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Mark DePristo 8562bfaae1 Optimize GenomeLocParser.createGenomeLoc 
-- The new version is roughly 2x faster than the previous version.  The key here was to cleanup the workflow for validateGenomeLoc and remove the now unnecessary synchronization blocks from the CachingSequencingDictionary, since these are now thread local variables
-- #resolves https://jira.broadinstitute.org/browse/GSA-724
 		2013-01-30 09:47:47 -05:00
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R Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
activeregion Cleanup, document, and unit test ActiveRegion 2013-01-30 09:47:12 -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 Fix the CachingIndexedFastaSequenceFileUnitTest 2013-01-29 21:07:16 -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 Collapse the downsampling fork in the GATK engine 2013-01-28 01:50:30 -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 Add join call to Progress meter unit test so we actually know the daemon thread has finished 2013-01-27 16:52:45 -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 Making SplitReads output FastQ's instead of BAM 2013-01-27 02:36:31 -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
variant Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
AutoFormattingTimeUnitTest.java AutoFormattingTimeUnitTest should be in utils 2013-01-30 09:47:47 -05:00
BitSetUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocParserBenchmark.java Optimize GenomeLocParser.createGenomeLoc 2013-01-30 09:47:47 -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
MWUnitTest.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -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