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Change in ordering for a disjunctions. Walker will no longer try to calculate number of simple mismatches in the pileup if the pileup includes 'N's. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1877 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-19 18:24:14 +00:00
parent 10bde9e77b
commit 055a99fb05
1 changed files with 1 additions and 1 deletions
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java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
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@ -222,7 +222,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
} }
public boolean baseIsUsable ( RefMetaDataTracker tracker, ReferenceContext ref, ReadBackedPileup pileup, AlignmentContext context ) { public boolean baseIsUsable ( RefMetaDataTracker tracker, ReferenceContext ref, ReadBackedPileup pileup, AlignmentContext context ) {
return pileupBelowMismatchThreshold(ref,pileup) && baseIsConfidentRef(tracker,ref,context) && pileupContainsNoNs(pileup); return pileupContainsNoNs(pileup) && baseIsConfidentRef(tracker,ref,context) && pileupBelowMismatchThreshold(ref,pileup);
} }
public boolean pileupBelowMismatchThreshold( ReferenceContext ref, ReadBackedPileup pileup ) { public boolean pileupBelowMismatchThreshold( ReferenceContext ref, ReadBackedPileup pileup ) {