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trivial change: toUpperCase no longer necessary 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3470 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-02 14:00:47 +00:00
parent 87fe60fe4f
commit 56e504789a
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -123,7 +123,7 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
if ( pileup != null ) { if ( pileup != null ) {
int mismatchQualities = 0, totalQualities = 0; int mismatchQualities = 0, totalQualities = 0;
char upperRef = Character.toUpperCase(ref.getBaseAsChar()); char refBase = (char)ref.getBase();
for (PileupElement p : pileup ) { for (PileupElement p : pileup ) {
// check the ends of the reads to see how far they extend // check the ends of the reads to see how far they extend
SAMRecord read = p.getRead(); SAMRecord read = p.getRead();
@ -136,7 +136,7 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
// look for mismatches // look for mismatches
else { else {
if ( Character.toUpperCase(p.getBase()) != upperRef ) if ( Character.toUpperCase(p.getBase()) != refBase )
mismatchQualities += p.getQual(); mismatchQualities += p.getQual();
totalQualities += p.getQual(); totalQualities += p.getQual();
} }