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arguments
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The default value for --contamination_fraction_to_filter is now 0.05 (5%) in both UG and HC. Users of GATK-lite get pushed down to 0% by default (since it's not enabled) or get a user error if they try to set it.
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2012-10-26 01:04:51 -04:00 |
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contexts
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Don't try to left align indels in unmapped reads (which for some reason can still have CIGARs) because the ref context is null.
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2012-08-29 15:01:11 -04:00 |
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datasources
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Missing file are user errors.
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2012-10-12 09:48:12 -04:00 |
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downsampling
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PerSampleDownsamplingReadsIterator: fix for incorrect use of DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL
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2012-09-21 22:43:39 -04:00 |
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examples
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Adding categories for the remaining uncategorized walkers
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2012-07-30 11:35:08 -04:00 |
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executive
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Retiring TraverseReads and TraverseLoci after testing confirms nano scheduler version in single threaded version is fine
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2012-10-22 16:55:06 -04:00 |
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filters
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Fix docs for BadMateFilter
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2012-10-12 08:35:45 -04:00 |
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io
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Fixed yet another NPE related to the ArgumentTypeDescriptor vs. ArgumentMatchValue. Added integration test based on GSA-621.
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2012-10-22 12:05:32 -04:00 |
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iterators
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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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phonehome
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New GATK argument interface for data and cpu threads
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2012-09-05 15:45:24 -04:00 |
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refdata
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Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers
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2012-08-30 10:15:10 -04:00 |
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report
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Ready for full-scale evaluation adaptive BQSR contexts
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2012-08-03 16:02:53 -04:00 |
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resourcemanagement
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Fixed bug in ThreadAllocation getTotalNumberOfThreads
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2012-09-05 16:35:32 -04:00 |
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samples
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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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traversals
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Retiring TraverseReads and TraverseLoci after testing confirms nano scheduler version in single threaded version is fine
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2012-10-22 16:55:06 -04:00 |
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walkers
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Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable
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2012-10-26 02:13:26 -04:00 |
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CommandLineExecutable.java
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Update URL for phone home / GATK key documentation output by the GATK upon error
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2012-08-08 09:29:54 -04:00 |
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CommandLineGATK.java
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Update the out of space error to include another permutation
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2012-10-12 09:38:12 -04:00 |
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GenomeAnalysisEngine.java
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Re-allow running the GATK with experimental downsampling
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2012-09-21 23:20:46 -04:00 |
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ReadMetrics.java
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Mark I NanoScheduling TraverseLoci
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2012-09-05 15:45:23 -04:00 |
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ReadProperties.java
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Experimental, downsampler-friendly read shard balancer
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2012-09-21 22:17:58 -04:00 |
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WalkerManager.java
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Downsampling: experimental engine integration
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2012-09-06 15:03:27 -04:00 |
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package-info.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 |
b06f689d4b