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R
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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activeregion
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Adaptations to accomodate Tribble API changes, comprising mostly of the following.
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2013-08-19 15:52:47 -04:00 |
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baq
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Fixing BQSR/BAQ bug:
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2013-01-31 11:03:17 -05:00 |
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classloader
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Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements
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2013-05-10 19:00:33 -04:00 |
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clipping
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Write a new tool for spliting reads that have N cigar string.
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2014-01-01 22:21:36 -05:00 |
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codecs/hapmap
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Adaptations to accomodate Tribble API changes, comprising mostly of the following.
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2013-08-19 15:52:47 -04:00 |
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collections
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Fixing license on Yossi's file
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2013-02-05 11:14:43 -05:00 |
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crypt
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Update expected test output for Java 7
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2013-05-01 16:18:01 -04:00 |
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fasta
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Move BaseUtils back to the GATK by request, along with associated utility methods
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2013-01-30 13:09:44 -05:00 |
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file
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Detect stuck lock-acquisition calls, and disable file locking for tests
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2013-04-24 22:49:02 -04:00 |
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fragments
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A whole slew of improvements to the Haplotype Caller and related code.
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2013-07-12 10:09:10 -04:00 |
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haplotype
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Major improvements to HC that trims down active regions before genotyping
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2013-04-08 12:47:49 -04:00 |
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interval
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Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists
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2013-04-02 14:01:52 -04:00 |
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io
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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locusiterator
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Working version of HaplotypeCaller ReferenceConfidenceModel that accounts for indels as well as SNP confidences
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2013-07-02 15:46:38 -04:00 |
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nanoScheduler
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Further tweaking of test timeouts
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2013-03-15 14:49:21 -04:00 |
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pileup
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Fixing ReadBackedPileup to represent mapping qualities as ints, not (signed) bytes.
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2013-07-23 23:47:15 -04:00 |
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progressmeter
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Subshard timeouts in the GATK
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2013-05-15 07:00:39 -04:00 |
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recalibration
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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report
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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runtime
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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sam
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Write a new tool for spliting reads that have N cigar string.
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2014-01-01 22:21:36 -05:00 |
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smithwaterman
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New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.
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2013-05-13 09:36:39 -04:00 |
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text
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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threading
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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variant
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Added some bug fixes to the gVCF merging code after finally getting some real data to play with.
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2014-01-08 08:34:35 -05:00 |
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AutoFormattingTimeUnitTest.java
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AutoFormattingTimeUnitTest should be in utils
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2013-01-30 09:47:47 -05:00 |
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BaseUtilsUnitTest.java
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More aggressive checking of AWS key quality upon startup in the GATK
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2013-01-31 09:08:38 -05:00 |
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BitSetUtilsUnitTest.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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GenomeLocParserBenchmark.java
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Optimize GenomeLocParser.createGenomeLoc
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2013-01-30 09:47:47 -05:00 |
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GenomeLocParserUnitTest.java
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Adding Graph-based likelihood ratio calculation to HC
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2013-12-02 19:37:19 -05:00 |
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GenomeLocSortedSetUnitTest.java
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Fixed the add functionality of GenomeLocSortedSet.
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2013-02-28 23:31:00 -05:00 |
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GenomeLocUnitTest.java
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Added distance across contigs calculation to GenomeLocs
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2013-02-07 16:31:41 -05:00 |
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MRUCachingSAMSequencingDictionaryUnitTest.java
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Refactoring and unit testing GenomeLocParser
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2013-01-30 09:47:47 -05:00 |
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MWUnitTest.java
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Move some VCF/VariantContext methods back to the GATK based on feedback
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2013-01-29 16:56:55 -05:00 |
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MathUtilsUnitTest.java
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Introducing the latest-and-greatest in genotyping: CalculatePosteriors.
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2013-11-27 13:00:45 -05:00 |
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MedianUnitTest.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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NGSPlatformUnitTest.java
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Expand NGSPlatform to meet SAM 1.4 spec, with full unit tests
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2013-02-09 11:16:21 -05:00 |
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PathUtilsUnitTest.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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QualityUtilsUnitTest.java
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Final edge case bug fixes to QualityUtil routines
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2013-02-16 07:31:38 -08:00 |
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SequenceDictionaryUtilsUnitTest.java
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Sequence dictionary validation: detect problematic contig indexing differences
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2013-02-25 11:14:22 -05:00 |
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SimpleTimerUnitTest.java
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Fix tests that were consistently or intermittently failing when run in parallel on the farm
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2013-03-06 13:56:54 -05:00 |
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UtilsUnitTest.java
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New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.
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2013-05-13 09:36:39 -04:00 |
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