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R
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No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
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2011-10-27 14:17:07 -04:00 |
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activeregion
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BQSR Gatherer implementation and integration tests
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2012-03-27 13:50:22 -05:00 |
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baq
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clipping
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Add support for reads starting with insertion
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2012-01-03 09:29:45 -05:00 |
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codecs
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Adding test for reading samtools VCF file
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2012-02-27 17:05:50 -05:00 |
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collections
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crypt
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Do not fail tests that require the GATK private key if the user does not have permission to read it
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2012-03-06 15:57:02 -05:00 |
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fasta
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fragments
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GATKSAMRecord refactor
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2011-11-03 15:43:26 -04:00 |
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genotype/vcf
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Change interface to getNegLog10PError to getLog10PError
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2011-11-18 21:07:30 -05:00 |
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interval
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make the size of a GenomeLoc int instead of long
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2012-02-03 17:12:42 -05:00 |
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io
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Public-key authorization scheme to restrict use of NO_ET
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2012-03-06 00:09:43 -05:00 |
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pileup
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GATKSAMRecord refactor
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2011-11-03 15:43:26 -04:00 |
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recalibration
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BQSR with GATKReport implementation
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2012-03-23 15:42:32 -04:00 |
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report
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runtime
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No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
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2011-10-27 14:17:07 -04:00 |
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sam
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BitSet implementation of the on-the-fly recalibration using the CSV format file.
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2012-03-16 13:02:15 -04:00 |
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text
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threading
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variantcontext
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Merged bug fix from Stable into Unstable
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2012-03-16 14:33:53 -04:00 |
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BaseUtilsUnitTest.java
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…
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BitSetUtilsUnitTest.java
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BitSets keys to lower BQSR's memory footprint
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2012-03-16 13:01:48 -04:00 |
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GenomeLocParserUnitTest.java
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During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.
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2011-11-17 13:56:42 -05:00 |
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GenomeLocSortedSetUnitTest.java
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GenomeLocUnitTest.java
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Support for list of known CNVs in VariantEval
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2011-11-30 17:05:16 -05:00 |
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HaplotypeUnitTest.java
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Minor misc updates
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2012-03-06 10:14:45 -05:00 |
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MWUnitTest.java
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MathUtilsUnitTest.java
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Forgot to add tolerance to new MathUtils unit tests
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2012-03-28 08:18:36 -04:00 |
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PathUtilsUnitTest.java
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QualityUtilsUnitTest.java
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Caching log calculations cut the non-Map runtime of HaplotypeCaller in half. Moved the qual log cache used in HC and PairHMM into a common place and added unit tests.
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2012-03-21 08:45:42 -04:00 |
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ReservoirDownsamplerUnitTest.java
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SimpleTimerUnitTest.java
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The right fix for this test is just to delete it.
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2011-11-15 14:53:27 -05:00 |
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UtilsUnitTest.java
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d2586911a4