From 940029fa5dd3539680ae3773619989a7b86ae32f Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 2 May 2012 14:05:08 -0400 Subject: [PATCH] Fixing on-the-fly recalibration (caught by Ryan) low quality bases in the tails were being turned to N's in the final read. --- .../sting/gatk/walkers/bqsr/ContextCovariate.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java index c5aabc64d..e2d2a3d1f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java @@ -64,20 +64,20 @@ public class ContextCovariate implements StandardCovariate { } @Override - public CovariateValues getValues(GATKSAMRecord read) { + public CovariateValues getValues(final GATKSAMRecord read) { int l = read.getReadLength(); BitSet[] mismatches = new BitSet[l]; BitSet[] insertions = new BitSet[l]; BitSet[] deletions = new BitSet[l]; - read = ReadClipper.clipLowQualEnds(read, LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS); // Write N's over the low quality tail of the reads to avoid adding them into the context + GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS); // Write N's over the low quality tail of the reads to avoid adding them into the context - final boolean negativeStrand = read.getReadNegativeStrandFlag(); - byte[] bases = read.getReadBases(); + final boolean negativeStrand = clippedRead.getReadNegativeStrandFlag(); + byte[] bases = clippedRead.getReadBases(); if (negativeStrand) bases = BaseUtils.simpleReverseComplement(bases); - for (int i = 0; i < read.getReadLength(); i++) { + for (int i = 0; i < clippedRead.getReadLength(); i++) { mismatches[i] = contextWith(bases, i, mismatchesContextSize); insertions[i] = contextWith(bases, i, insertionsContextSize); deletions[i] = contextWith(bases, i, deletionsContextSize);