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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Mark DePristo 6d22485a4c Critical bugfix to ReduceRead functionality of the GATKSAMRecord 
-- The function getReducedCounts() was returning the undecoded reduced read tag, which looks like [10, 5, -1, -5] when the depths were [10, 15, 9, 5].  The only function that actually gave the real counts was getReducedCount(int i) which did the proper decoding.  Now GATKSAMRecord decodes the tag into the proper depths vector so that getReduceCounts() returns what one reasonably expects it to, and getReduceCount(i) merely looks up the value at i.  Added unit test to ensure this behavior going forward.
-- Changed the name of setReducedCounts() to setReducedCountsTag as this function assumes that counts have already been encoded in the tag way.
 		2013-04-08 12:47:50 -04:00
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R Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
activeregion Major improvements to HC that trims down active regions before genotyping 2013-04-08 12:47:49 -04:00
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 New GATKSAMRecord concept of a strandless read, update to FS 2013-03-13 11:16:36 -04:00
haplotype Major improvements to HC that trims down active regions before genotyping 2013-04-08 12:47:49 -04:00
haplotypeBAMWriter Move Haplotype class to its own package in utils 2013-04-08 12:47:47 -04:00
interval Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists 2013-04-02 14:01:52 -04:00
io Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
locusiterator LIBS unit test debugging should be false 2013-04-08 12:47:47 -04:00
nanoScheduler Further tweaking of test timeouts 2013-03-15 14:49:21 -04:00
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 Critical bugfix to ReduceRead functionality of the GATKSAMRecord 2013-04-08 12:47:50 -04:00
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 AssessNA12878 bugfixes 2013-03-18 15:48:08 -04:00
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 Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -05:00
GenomeLocUnitTest.java Added distance across contigs calculation to GenomeLocs 2013-02-07 16:31:41 -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 Rarely-occurring logic bugfix for GenotypeConcordance, streamlining and testing of MathUtils 2013-03-28 23:25:28 -04:00
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
SequenceDictionaryUtilsUnitTest.java Sequence dictionary validation: detect problematic contig indexing differences 2013-02-25 11:14:22 -05:00
SimpleTimerUnitTest.java Fix tests that were consistently or intermittently failing when run in parallel on the farm 2013-03-06 13:56:54 -05:00
UtilsUnitTest.java Cleanup of FragmentUtils 2013-03-13 07:36:20 -04:00