hanna d4ee999ef9 Creates files supplemental to the reference sequence, consumed by BWA. ... ANN - Alternate form of the sequence dictionary. Should be created from a sequence dictionary with full contig names. AMB - A map of 'holes' in the genome, aka runs of non-ACGTacgt bases. This skeletal implementation always reports no holes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2455 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-28 21:40:44 +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	Creates files supplemental to the reference sequence, consumed by BWA.	2009-12-28 21:40:44 +00:00
test/org/broadinstitute/sting	Sites that were marked NO_DINUC no longer get dinuc-corrected but are still recalibrated using the other available covariates. Solid cycle is now the same as Illumina cycle pending an analysis that looks at the effect of PrimerRoundCovariate. Solid color space methods cleaned up to reduce number of calls to read.getAttribute(). Polished NHashMap sort method in preparation for move to core/utils. Added additional plots in AnalyzeCovariates to look at reported quality as a function of the covariate.	2009-12-28 20:19:37 +00:00