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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2012-01-03 18:10:39 -05:00
parent 2c3a9ce02f 9b55505c03
commit 9ff8a01da2
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.Cigar;
import net.sf.samtools.CigarElement; import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator; import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; 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.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Allele;
@ -409,9 +409,9 @@ public class PairHMMIndelErrorModel {
} }
} }
else { else {
//System.out.format("%d %s\n",p.getRead().getAlignmentStart(), p.getRead().getClass().getName()); // System.out.format("%d %s\n",p.getRead().getAlignmentStart(), p.getRead().getClass().getName());
SAMRecord read = ReadClipper.hardClipAdaptorSequence(p.getRead()); GATKSAMRecord read = ReadClipper.hardClipAdaptorSequence(p.getRead());
if (read == null) if (read.isEmpty())
continue; continue;
if(ReadUtils.is454Read(read)) { if(ReadUtils.is454Read(read)) {