From b3cc04976f662af2283dae5664640bec7343ca92 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 8 Oct 2012 10:18:29 -0400 Subject: [PATCH] Fixing BQSR bug reported on the forum for reads that being with insertions. --- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 91d982f20..49bfc6e06 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -197,15 +197,15 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed } } - private boolean readHasBeenSkipped(GATKSAMRecord read) { + private boolean readHasBeenSkipped( final GATKSAMRecord read ) { return read.containsTemporaryAttribute(SKIP_RECORD_ATTRIBUTE); } - private boolean isLowQualityBase(GATKSAMRecord read, int offset) { - return read.getBaseQualities()[offset] < minimumQToUse; + private boolean isLowQualityBase( final PileupElement p ) { + return p.getQual() < minimumQToUse; } - private boolean readNotSeen(GATKSAMRecord read) { + private boolean readNotSeen( final GATKSAMRecord read ) { return !read.containsTemporaryAttribute(SEEN_ATTRIBUTE); } @@ -225,7 +225,7 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed final GATKSAMRecord read = p.getRead(); 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; if (readNotSeen(read)) {