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More misc cleanup

This commit is contained in:
Eric Banks 2012-07-03 14:55:37 -04:00
parent 344c3aeb1d
commit 617eebd204
1 changed files with 0 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java
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@ -82,7 +82,6 @@ public class ContextCovariate implements StandardCovariate {
@Override @Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) { public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
// TODO -- wrong: fix me
final 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 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 = clippedRead.getReadNegativeStrandFlag(); final boolean negativeStrand = clippedRead.getReadNegativeStrandFlag();