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gatk-3.8/java/test/org/broadinstitute/sting
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chartl 480859db50 Contractified version of MannWhitneyU. Some behavior has been changed: 
- Running a test when there are no observations of at least one of the sets now breaks the MWU contract
   + MWU returns Pair(Double.NaN,Double.NaN) in these instances to maintain the contract of never returning null
   + No more Double.Infinity values will appear
 - RankSumTests now probe the return values for NaNs, and don't annotate if they appear
 - For small sets where the probability is calculated recursively, the z-value is now the inversion of the error function
    and not the approximate z-value
 - UG and Annotator integration tests updated to reflect changes



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5845 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-05-23 13:57:15 +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 Contractified version of MannWhitneyU. Some behavior has been changed: 2011-05-23 13:57:15 +00:00
jna Added pipeline for calling FCP in batches called MultiFullCallingPipeline. 2011-02-15 18:26:14 +00:00
oneoffprojects/walkers Contractified version of MannWhitneyU. Some behavior has been changed: 2011-05-23 13:57:15 +00:00
playground/gatk/walkers PLEASE READ ME! In order to prepare for the upcoming changes to VCF4, we felt it was best to split up the vcf3 and vcf4 codecs (vcf4 is not backwards compatible to vcf3 and certain changes are too complex to handle in both codecs). Using the 'VCF' rod type in the GATK will now throw a UserException for vcf3.2 or vcf3.3 files telling you to use the 'VCF3' type instead (and vice versa). Integration/unit tests have been updated. For programmers: note that there is currently a lot of code duplication in the two codecs (although I pulled out the easy stuff to a VCFCodecUtils class); however WE ARE FREEZING THE VCF3 CODEC AND WILL NO LONGER MAKE CHANGES TO IT. All updates/improvements will be targetted to the vcf4 codec only as vcf3 is there only to be able to read legacy files. People should really be using vcf4 files only. 2011-05-11 12:07:44 +00:00
utils Contracts for SimpleTimer, as well as UnitTests 2011-05-22 19:45:31 +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 Added a utility method to retrieve the contig lengths for WG chunking. 2011-04-20 19:22:21 +00:00