chartl 3b1fabeff0 Major code refactoring: ... @ Pooled utils & power - Removed two of the power walkers leaving only PowerBelowFrequency, added some additional flags on PowerBelowFrequency to give it some of the behavior that PowerAndCoverage had - Removed a number of PoolUtils variables and methods that were used in those walkers or simply not used - Removed AnalyzePowerWalker (un-necessary) - Changed the location of Quad/Squad/ReadOffsetQuad into poolseq @NQS - Deleted all walkers but the minimum NQS walker, refactored not to use LocalMapType @ BaseTransitionTable - Added a slew of new integration tests for different flaggable and integral parameters - (Scala) just a System.out that was added and commented out (no actual code change) - (Java) changed a < to <= and a boolean formula Chris git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1887 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-20 14:58:04 +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	Major code refactoring:	2009-10-20 14:58:04 +00:00
test/org/broadinstitute/sting	Major code refactoring:	2009-10-20 14:58:04 +00:00