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R
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Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.
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2012-04-17 14:22:48 -04:00 |
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activeregion
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ActiveRegionWalker's isActive function returns a results object now instead of just a double.
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2012-07-27 11:01:39 -04:00 |
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baq
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clipping
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Updated and more thorough version of the BadCigar read filter
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2012-08-17 17:05:27 -04:00 |
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codecs
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GSA-485: Remove repairVCFHeader from GATK codebase
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2012-08-16 13:03:13 -04:00 |
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collections
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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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Ensure thread-safety of CachingIndexedFastaSequenceFile
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2012-08-27 12:11:54 -04:00 |
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fragments
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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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nanoScheduler
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Fix some of the broken integration tests
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2012-10-26 11:23:44 -04:00 |
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pileup
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recalibration
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Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table.
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2012-09-20 14:14:34 -04:00 |
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report
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runtime
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sam
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Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"
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2012-09-10 15:52:39 -04:00 |
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text
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Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.
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2012-04-17 14:22:48 -04:00 |
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threading
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Disable EfficiencyMonitoringThreadFactoryUnitTest
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2012-10-21 12:43:46 -04:00 |
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variantcontext
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Fixing the VariantContextUtilsUnitTest
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2012-09-22 23:24:55 -04:00 |
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BaseUtilsUnitTest.java
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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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GenomeLocUnitTest.java
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Bugfix to compareTo and equals in GenomeLoc
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2012-08-30 19:41:49 -04:00 |
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HaplotypeUnitTest.java
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Bug fixes related to the changes in allele padding. If a haplotype started with an insertion it led to array index out of bounds. Haplotype allele insert function is now very simple because all alleles are treated the same way. HaplotypeUnitTest now uses a variant context instead of creating Allele objects directly.
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2012-08-05 12:29:10 -04:00 |
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LegacyReservoirDownsamplerUnitTest.java
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Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"
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2012-09-10 15:52:39 -04:00 |
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MWUnitTest.java
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A couple of minor things.
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2012-09-20 12:48:13 -04:00 |
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MathUtilsUnitTest.java
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Increasing the precision of MathUtils.approximateLog10SumLog10 from 1E-3 to 1E-4. Genotyper integration tests change as a result. Expanding the unit tests of MathUtils.log10sumLog10.
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2012-10-15 13:24:32 -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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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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SimpleTimerUnitTest.java
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Done GSA-539: SimpleTimer should use System.nanoTime for nanoSecond resolution
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2012-09-05 15:45:23 -04:00 |
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UtilsUnitTest.java
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