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gatk-3.8/java/test/org/broadinstitute/sting
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depristo cd8321cdc9 Removed the completely unused generic but extremely expensive infrastructure for dynamic LocusIteratorFilters. Now the one, and probably only useful one, is called directly in the LocusIteratorByState itself to filter adaptor bases from reads. This shaves 10% off the runtime of all walkers, apparently. Has the additional benefit of eliminating a lot of complex infrastructure that resulted ultimately in only a single function call. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5525 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-03-27 20:48:24 +00:00
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alignment Quick fix for Danny Lieber: flesh out the additional functionality required 2011-01-31 05:28:37 +00:00
commandline Fixed long-standing bug reported by Mauricio where @Arguments assigned to 2011-01-12 22:18:24 +00:00
datasources/pipeline Removed deprecated getDbsnpFile. 2011-02-08 21:12:15 +00:00
gatk Removed the completely unused generic but extremely expensive infrastructure for dynamic LocusIteratorFilters. Now the one, and probably only useful one, is called directly in the LocusIteratorByState itself to filter adaptor bases from reads. This shaves 10% off the runtime of all walkers, apparently. Has the additional benefit of eliminating a lot of complex infrastructure that resulted ultimately in only a single function call. 2011-03-27 20:48:24 +00:00
jna Added pipeline for calling FCP in batches called MultiFullCallingPipeline. 2011-02-15 18:26:14 +00:00
oneoffprojects/walkers Fixed an edge case where an exception was thrown if either of the sets was empty for the MWU test. Also altered the output format so U itself is not printed (which though interesting, isn't so useful for recalibration), but rather a value I call V (really the deviation of U from its expectation). 2011-03-22 16:28:44 +00:00
playground/gatk/walkers Now uses the NO_HEADER option to avoid breaking MD5s due to changes in GATKArgumentCollection 2011-03-26 12:00:37 +00:00
utils Enabled the parameterize option for debugging PipelineTest MD5s. 2011-03-26 00:41:47 +00:00
BaseTest.java Added pipeline for calling FCP in batches called MultiFullCallingPipeline. 2011-02-15 18:26:14 +00:00
StingTextReporter.java Cleanup testng listener configuration. 2010-11-15 23:43:14 +00:00
WalkerTest.java When subsetting by sample, need to take extra care that hom-ref sites don't accidentally get treated as variant sites in CompOverlap. Renamed convenience method for creating command-lines in integration tests. 2011-02-18 06:26:38 +00:00