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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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Bugfix for GSA-647 HaplotypeCaller misses good variant because the active region doesn't trigger for an exome
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2012-11-01 15:34:04 -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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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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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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Work on GSA-508 / CachingIndexedFastaReader should internally upper case bases loading data
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2012-11-01 15:34:03 -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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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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GATKSAMRecord refactor
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2011-11-03 15:43:26 -04:00 |
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recalibration
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The user can now set the maximum allowable cycle on the command-line with --maximum_cycle_value. This value is (now) enforced in the Cycle covariate and a User Error is thrown if the maximum value is passed (with a helpful error message). Added unit tests to cover this new functionality.
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2012-11-20 22:41:57 -05:00 |
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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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Downsampling: experimental engine integration
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2012-09-06 15:03:27 -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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Disable EfficiencyMonitoringThreadFactoryUnitTest
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2012-10-21 12:43:46 -04:00 |
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variantcontext
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Adding 80% support for multi-allelic variants
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2012-11-21 17:24:59 -05:00 |
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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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Fix for GSA-649: GenomeLocSortedSet.overlaps is crazy slow. Also improved GenomeLocSortedSet.sizeBeforeLoc.
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2012-11-27 01:07:00 -05:00 |
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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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Lots more GGA fixes for the HC now that I understand what's going on internally. Integration tests pass except for the GGA test which I believe now produces better results.
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2012-11-20 16:13:29 -05:00 |
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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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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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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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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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