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R
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AggregateMetrics:
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2012-04-17 11:45:32 -04:00 |
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activeregion
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Fixing ActivityProfile unit test.
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2012-04-10 15:28:27 -04:00 |
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baq
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Putative fix for BAQ array out of bounds
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2011-09-21 11:25:08 -04:00 |
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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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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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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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Reduced the number of combinations being tested here, which was overkill
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2011-09-01 10:42:43 -04:00 |
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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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When constructing VariantContexts from symbolic alleles, check for the END tag in the INFO field; if present, set the stop position of the VC accordingly. Added integration test to ensure that this is working properly for use with -L intervals.
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2012-04-04 10:57:05 -04:00 |
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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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Adding engine capability to quantize qualities.
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2012-04-08 21:07:51 -04:00 |
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report
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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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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AggregateMetrics:
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2012-04-17 11:45:32 -04:00 |
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threading
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Removed GATK use of distributed parallelism framework.
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2011-07-20 16:26:09 -04:00 |
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variantcontext
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Modified UnitTests to respect reference padding
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2012-04-06 16:27:20 -04:00 |
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BaseUtilsUnitTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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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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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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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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Moved the Smith-Watermaning of haplotypes to earlier in the process so that alleles sent to genotyping would have the exact genomic sequence of the active region they represent. As a side effect cleaned up some edge case problems with variants, both real and false, which show up on the edges of active regions. Removed code that was replicated between the Haplotype class and ReadUtils. Finally figured out how to ensure that the indel calls coming out of the HC were left aligned.
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2012-04-04 16:04:29 -04:00 |
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MWUnitTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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MathUtilsUnitTest.java
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minor misc optimizations to PairHMM
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2012-04-18 15:02:26 -04:00 |
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PairHMMUnitTest.java
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Rebasing
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2012-04-18 20:05:43 -04:00 |
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PathUtilsUnitTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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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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Moving reduced read functionality into GATKSAMRecord
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2011-10-21 13:28:05 -04:00 |
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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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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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