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
..
gatk	ensure that in the indel case we don't allow identification as both an insertion and deletion at the same location in the VCF ROD	2009-10-19 18:21:00 +00:00
playground/gatk/walkers	Major code refactoring:	2009-10-20 14:58:04 +00:00
utils	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +00:00
BaseTest.java	Added some code to change the instrumentation for tests.	2009-05-20 05:15:27 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	Softclipping support in clip reads walker. Minor improvement to WalkerTest -- now can specify file extensions for tmp files. Matt -- I couldn't easily create non-presorted SAM file. The softclipper has an impact on this.	2009-10-19 21:54:53 +00:00