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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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Fixing unit test
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2012-07-06 12:08:09 -04:00 |
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codecs
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Updates to VCF processing for better BCF processing
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2012-07-08 15:44:33 -07:00 |
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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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Cleanup of VCF header lines and constants, BCF2 bugfixes
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2012-06-21 15:16:31 -04:00 |
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fasta
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A few misc. residual errors in last commit
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2012-06-21 16:04:25 -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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interval
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Refactored parsing of Rod/IntervalBinding. Queue S/G now uses all interval arguments passed to CommandLineGATK QFunctions including support for BED/tribble types, XL, ISR, and padding.
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2012-06-27 01:15:22 -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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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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Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped
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2012-04-27 09:58:38 -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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Updates to VCF processing for better BCF processing
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2012-07-08 15:44:33 -07:00 |
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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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NestedHashMap-based implementation of BQSRv2 along with a few minor optimizations. Not a huge runtime upgrade over the long bitset approach, but it allows us to implement further optimizations going forward. Integration test change because the original version had a bug in the quantized qual table creation.
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2012-06-27 16:55:49 -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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Adding genotype given alleles mode to the HaplotypeCaller.
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2012-05-30 15:07:01 -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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MedianUnitTest.java
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Final updates to integration tests for BCF2
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2012-05-24 10:58:59 -04:00 |
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PairHMMUnitTest.java
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Resolve merge conflicts
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2012-04-18 16:25:03 -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 |
f657b8bda8