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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Mark DePristo 206eab80e3 Expanded unit tests for AlignmentUtils 
-- Added JIRA entries for the remaining capabilities to be fixed up and unit tested
 		2013-02-01 13:51:31 -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 Fixing BQSR/BAQ bug: 2013-01-31 11:03:17 -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 Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -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 Expanded unit tests for AlignmentUtils 2013-02-01 13:51:31 -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
BaseUtilsUnitTest.java More aggressive checking of AWS key quality upon startup in the GATK 2013-01-31 09:08:38 -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 Refactoring the SimpleGenomeLoc into the now public utility UnvalidatingGenomeLoc and the RR-specific FinishedGenomeLoc. 2013-01-30 10:45:29 -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 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