chartl a32245f7d2 Modifications: ... QualityUtils - Stole the BaseUtils code for flipping reads around and applied it to quality scores SecondBaseSkew - Nothing's really different, just a commented line Additions (experimental annotations for future development of second-base annotation) ** I DO NOT INTEND FOR ANYONE TO USE THESE ** - ProportionOfNonrefBasesSupportingSNP - ProportionOfSNPSecondBasesSupportingRef - ProportionOfRefSecondBasesSupportingSNP + I hope these are self-explanatory - QualityAdjustedSecondBaseLod + Adjust lod-score by 10*log10[P[second bases are as observed]] Added walker: QualityScoreByStrand - oneoff project that's being saved if i ever need it git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2527 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-06 19:18:07 +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	Modifications:	2010-01-06 19:18:07 +00:00
test/org/broadinstitute/sting	Temporary command-line support to enable rod walkers, if you know what you are doing this is safe.	2010-01-06 12:15:36 +00:00