asivache 5202d959bf NM attribute changed in sam jdk (?) from Integer to Short, or maybe it is presented differently by the reader depending on whether SAM or BAM is processed; in any case, both Integer and Short are safe now ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1522 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-03 19:03:32 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	NM attribute changed in sam jdk (?) from Integer to Short, or maybe it is presented differently by the reader depending on whether SAM or BAM is processed; in any case, both Integer and Short are safe now	2009-09-03 19:03:32 +00:00
test/org/broadinstitute/sting	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