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Fixing BQSR bug reported on the forum for reads that being with insertions.

This commit is contained in:
Ryan Poplin 2012-10-08 10:18:29 -04:00
parent 365f1d2429
commit b3cc04976f
1 changed files with 5 additions and 5 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -197,15 +197,15 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
} }
} }
private boolean readHasBeenSkipped(GATKSAMRecord read) { private boolean readHasBeenSkipped( final GATKSAMRecord read ) {
return read.containsTemporaryAttribute(SKIP_RECORD_ATTRIBUTE); return read.containsTemporaryAttribute(SKIP_RECORD_ATTRIBUTE);
} }
private boolean isLowQualityBase(GATKSAMRecord read, int offset) { private boolean isLowQualityBase( final PileupElement p ) {
return read.getBaseQualities()[offset] < minimumQToUse; return p.getQual() < minimumQToUse;
} }
private boolean readNotSeen(GATKSAMRecord read) { private boolean readNotSeen( final GATKSAMRecord read ) {
return !read.containsTemporaryAttribute(SEEN_ATTRIBUTE); return !read.containsTemporaryAttribute(SEEN_ATTRIBUTE);
} }
@ -225,7 +225,7 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
final GATKSAMRecord read = p.getRead(); final GATKSAMRecord read = p.getRead();
final int offset = p.getOffset(); final int offset = p.getOffset();
if (readHasBeenSkipped(read) || isLowQualityBase(read, offset)) // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases) if (readHasBeenSkipped(read) || isLowQualityBase(p)) // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases)
continue; continue;
if (readNotSeen(read)) { if (readNotSeen(read)) {