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gatk-3.8/java/test/org/broadinstitute/sting
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chartl 328f89f66a Minor changes to MannWhitneyU: 
- Comment fixes to better explain why two-sided test wants to use the LOWER (not higher) value for U
 - Much more direct testing of MWU functions
 - Uniform approximation was always using the < cumulant (sometimes the > cumulant should be used instead)
 - Uniform approximation currently not used (regime in which it was being used was not the right one -- not necessarily bad, but not an improvement over normal)
    + this particular approximation is for major imbalances of the form m >> n. Code may be altered in the future to use this method for this particular regime, if the method's not too slow.
 - Hook into one-sided test.

RegionalAssociationRecalibrator: NaNs were being caused by presence of Infinity and -Infinity values out of the walker. Currently I'm just re-setting them to arbitrary post-whitened values, but the walker will be changed to prevent output of these values, and the "fix" will undone.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5539 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-03-30 17:03:02 +00:00
..
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 Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately. 2011-03-29 21:04:09 +00:00
jna Added pipeline for calling FCP in batches called MultiFullCallingPipeline. 2011-02-15 18:26:14 +00:00
oneoffprojects/walkers Minor changes to MannWhitneyU: 2011-03-30 17:03:02 +00:00
playground/gatk/walkers Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately. 2011-03-29 21:04:09 +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