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Dumb, dumb bug. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@672 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-05-12 19:21:33 +00:00
parent 6e69193e3c
commit 4c12df372c
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java
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@ -90,7 +90,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
int sum = 0;
for ( int readIndex = 0 ; readIndex < read.length() ; readIndex++, refIndex++ ) {
if ( refIndex > ref.length() )
if ( refIndex >= ref.length() )
sum += MAX_QUAL;
else if ( Character.toUpperCase(read.charAt(readIndex)) != Character.toUpperCase(ref.charAt(refIndex)) )
sum += (int)quals.charAt(readIndex) - 33;