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Fixing PairHMMIndelErrorModel array out of bounds 

This error was due to the ReadClipper change of contract. Before the read utils would return null if a read was entirely clipped, now it returns an empty (safe) GATKSAMRecord.
This commit is contained in:
Mauricio Carneiro 2012-01-03 18:08:46 -05:00
parent ea6e718cb8
commit 9b55505c03
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -28,13 +28,13 @@ package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
@ -409,9 +409,9 @@ public class PairHMMIndelErrorModel {
}
}
else {
//System.out.format("%d %s\n",p.getRead().getAlignmentStart(), p.getRead().getClass().getName());
SAMRecord read = ReadClipper.hardClipAdaptorSequence(p.getRead());
if (read == null)
// System.out.format("%d %s\n",p.getRead().getAlignmentStart(), p.getRead().getClass().getName());
GATKSAMRecord read = ReadClipper.hardClipAdaptorSequence(p.getRead());
if (read.isEmpty())
continue;
if(ReadUtils.is454Read(read)) {