asivache 499b3536a4 Changed to use AlignmentUtils.isReadUnmapped() for better consistency with SAM spec; also, it is now explicitly enforced that unmapped reads have <NO_...> values set for ref contig and start upon "remapping" ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1519 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-03 16:45:07 +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	Changed to use AlignmentUtils.isReadUnmapped() for better consistency with SAM spec; also, it is now explicitly enforced that unmapped reads have <NO_...> values set for ref contig and start upon "remapping"	2009-09-03 16:45:07 +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