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Aligner.xml
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Cleanup and formatting overhaul.
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2010-01-21 19:22:56 +00:00 |
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AnalyzeCovariates.xml
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A few more bug fixes based on extended testing. Sorry, Eric.
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2010-01-21 22:12:16 +00:00 |
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CreatePackager.xsl
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Added JavaMail dependencies to Queue package since bcel wasn't picking them up.
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2011-04-23 20:48:40 +00:00 |
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FindContaminatingReadGroups.xml
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Cleanup and formatting overhaul.
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2010-01-21 19:22:56 +00:00 |
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GATK-Picard.xml
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A few more bug fixes based on extended testing. Sorry, Eric.
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2010-01-21 22:12:16 +00:00 |
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GATKEngine.xml
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Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.
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2011-03-24 14:03:51 +00:00 |
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GATKResources.xml
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/broad/1KG doesn't exist
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2010-10-06 12:54:38 +00:00 |
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GenomeAnalysisTK.xml
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Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.
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2011-03-24 14:03:51 +00:00 |
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IndelGenotyper.xml
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Bringing IndelGenotyper back to life
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2010-02-03 20:12:49 +00:00 |
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LocalRealignmentAroundIndels.xml
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Since IntervalCleaner is gone for good, it is sensible to update the package to refer to the new IndelRealigner instead
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2010-02-24 16:42:56 +00:00 |
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PicardPrivate.xml
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Oops. Failed to add DbSnpMatchMetrics to Picard private jar.
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2011-06-14 15:14:19 +00:00 |
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QualityScoresRecalibration.xml
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A few more bug fixes based on extended testing. Sorry, Eric.
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2010-01-21 22:12:16 +00:00 |
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Queue.xml
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Added cofoja to the Queue package. Although BCEL doesn't think they're needed the scala compiler respectfully disagrees.
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2011-05-26 17:42:34 +00:00 |
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RMDIndexer.xml
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include the codecs into the RMD indexer that are available in the GATK, not just Tribble
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2010-11-11 06:35:04 +00:00 |
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UnifiedGenotyper.xml
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Cleanup and formatting overhaul.
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2010-01-21 19:22:56 +00:00 |
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VariantAnnotator.xml
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Include all standard annotations
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2010-10-11 20:52:08 +00:00 |
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VariantEval.xml
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Add CountFunctionalVariants to local release (for firehose)
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2010-07-17 01:36:16 +00:00 |
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VariantFiltration.xml
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Temporary solution: add the commons logging implementation to the VariantFiltration package. Downstream solution is described in GSA-262.
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2010-01-23 01:46:18 +00:00 |
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VariantRecalibration.xml
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VariantOptimizer package is moved to core, renamed as VariantRecalibration, and added to the binary release package. VariantOptimizer walker is renamed to GenerateVariantClustersWalker and ApplyVariantClustersWalker renamed to VariantRecalibrator. Integration tests added, performance tests still to be done.
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2010-05-28 18:20:18 +00:00 |
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