Eric Banks e48f754478 Fixes to several of the annotations for reduced reads (and other issues). ... 1. Have the RMSMappingQuality annotation take into account the fact that reduced reads represent multiple reads. 2. The rank sume tests should not be using reduced reads (because they do not represent distinct observations). 3. Fixed a massive bug in the BaseQualityRankSumTest annotation! It was not using the base qualities but rather the read likelihoods?! Added a unit test for Rank Sum Tests to prove that the distributions are correctly getting assigned appropriate p-values. Also, and just as importantly, the test shows that using reduced reads in the rank sum tests skews the results and makes insignificant distributions look significant (so it can falsely cause the filtering of good sites). Also included in this commit is a massive refactor of the RankSumTest class as requested by the reviewer.		2013-06-16 01:18:20 -04:00
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java	Fixes to several of the annotations for reduced reads (and other issues).	2013-06-16 01:18:20 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00