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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Mark DePristo 3b67aa8aee Final edge case bug fixes to QualityUtil routines 
-- log10 functions in QualityUtils allow -Infinity to allow log10(0.0) values
-- Fix edge condition of log10OneMinusX failing with Double.MIN_VALUE
-- Fix another edge condition of log10OneMinusX failing with a small but not min_value double
 		2013-02-16 07:31:38 -08:00
..
R Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
activeregion Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -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 Fixing license on Yossi's file 2013-02-05 11:14:43 -05:00
crypt Update MD5s to reflect version number change in the BAM header 2013-02-01 13:51:31 -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 Update MD5s to reflect version number change in the BAM header 2013-02-01 13:51:31 -05:00
io Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
locusiterator Cleanup and unit tests for QualityUtils 2013-02-16 07:31:37 -08:00
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 Resolves Genome Sequence Analysis GSA-750 Don't print an endless series of starting messages from the ProgressMeter 2013-02-04 15:47:30 -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 PrintReads writes a header when used with -BQSR 2013-02-14 22:19:14 -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 Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -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 Added distance across contigs calculation to GenomeLocs 2013-02-07 16:31:41 -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
NGSPlatformUnitTest.java Expand NGSPlatform to meet SAM 1.4 spec, with full unit tests 2013-02-09 11:16:21 -05:00
PathUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
QualityUtilsUnitTest.java Final edge case bug fixes to QualityUtil routines 2013-02-16 07:31:38 -08:00
SimpleTimerUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
UtilsUnitTest.java Cleanup unused utils functions, and add unit test for one (append) 2013-02-01 13:51:31 -05:00