From 055a99fb0540fc96591de8e1d0dca5a43bbdbcb1 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 19 Oct 2009 18:24:14 +0000
Subject: [PATCH] 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
---
 .../gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
index db3dc5abf..9dd056388 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
@@ -222,7 +222,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
     }
 
     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 ) {