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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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Added checking in the GATK for mis-encoded quality scores.
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2012-12-03 11:18:41 -05:00 |
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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/hapmap
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Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
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2012-12-19 10:25:22 -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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NanoScheduler optimizations and simplification
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2012-12-24 13:35:57 -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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Enabling the Recal Report unit test (which looks like it was never ever enabled)
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2012-12-26 15:35:50 -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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Quick fix: base qual array in the GATKSAMRecord stores the actual phred values (-33) and not the original bytes (duh).
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2012-12-03 12:18:20 -05:00 |
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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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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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Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
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2012-12-19 10:25:22 -05:00 |
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LegacyReservoirDownsamplerUnitTest.java
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Use the new downsampling implementation by default
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2012-12-10 09:44:50 -05:00 |
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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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