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Bugfix. isMismatch() was actually computing isMatch(). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1743 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-09-29 20:04:59 +00:00
parent e28b45688c
commit 281a77c981
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSClusteredZScoreWalker.java
View File

@ -73,7 +73,7 @@ public class NQSClusteredZScoreWalker extends LocusWalker<LocalMapType, int[][][
}
public boolean isMismatch( SAMRecord read, int offset, ReferenceContext ref ) {
return ((char) read.getReadBases()[offset]) == ref.getBase();
return (Character.toUpperCase((char) read.getReadBases()[offset]) != ref.getBase());
}
public int getQScoreAsInt( SAMRecord read, int offset ) {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/NQSCovariantByCountsWalker.java
View File

@ -111,7 +111,7 @@ public class NQSCovariantByCountsWalker extends LocusWalker< LocalMapType, int[]
}
public boolean isMismatch( SAMRecord read, int offset, ReferenceContext ref ) {
return ( ((char)read.getReadBases()[offset]) == ref.getBase() );
return ( Character.toUpperCase((char)read.getReadBases()[offset]) != ref.getBase() );
}
public String header() {