zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/public/java/test/org/broadinstitute/sting/utils
History
Mark DePristo 45603f58cd Refactoring and unit testing GenomeLocParser 
-- Moved previously inner class to MRUCachingSAMSequenceDictionary, and unit test to 100% coverage
-- Fully document all functions in GenomeLocParser
-- Unit tests for things like parsePosition (shocking it wasn't tested!)
-- Removed function to specifically create GenomeLocs for VariantContexts.  The fact that you must incorporate END attributes in the context means that createGenomeLoc(Feature) works correctly
-- Depreciated (and moved functionality) of setStart, setStop, and incPos to GenomeLoc
-- Unit test coverage at like 80%, moving to 100% with next commit
 		2013-01-30 09:47:47 -05:00
..
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 Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -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
MRUCachingSAMSequencingDictionaryUnitTest.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -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