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tell UnifiedGenotyper to return calls at all bases 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1941 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2009-10-30 03:10:44 +00:00
parent 4ee1d6f733
commit 4bdb5b03bd
1 changed files with 1 additions and 0 deletions
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java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
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@ -64,6 +64,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
ug.initialize();
uac.baseModel = BaseMismatchModel.THREE_STATE;
uac.ALL_BASES = true;
ug.setUnifiedArgumentCollection(uac);
// refWindow = new ReferenceContextWindow(nPreviousBases);
usePreviousBases = new ArrayList<Boolean>();