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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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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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I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever).
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2012-11-27 10:26:17 -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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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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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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Fix failing unit tests for VariantContextUtilsUnitTest
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2012-11-27 14:26:23 -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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Fixing parsing of genomelocs that contain colons in the contig names (which is allowed by the spec) as reported on the forum. Added unit test for this case.
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2012-11-27 11:00:33 -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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