depristo 49a7babb2c Better organization of Genotype likelihood calculations. NewHotness is now just GenotypeLikelihoods. There are 1, 3, and empirical base error models available as subclasses, along with a simple way to make this (see the factory). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1481 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-30 19:16:30 +00:00
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genotyper	Better organization of Genotype likelihood calculations. NewHotness is now just GenotypeLikelihoods. There are 1, 3, and empirical base error models available as subclasses, along with a simple way to make this (see the factory).	2009-08-30 19:16:30 +00:00
indels	General-purpose management of output streams.	2009-08-23 00:56:02 +00:00
recalibration	Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5)	2009-08-28 14:14:21 +00:00
PrintReadsWalkerTest.java	Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.	2009-06-11 18:13:22 +00:00