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Misc minor cleanup

This commit is contained in:
Eric Banks 2011-11-14 09:41:54 -05:00
parent b7c33116af
commit 3d2970453b
3 changed files with 3 additions and 5 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
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@ -6,9 +6,7 @@ import org.broadinstitute.sting.utils.NGSPlatform;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.Arrays;
import java.util.EnumSet; import java.util.EnumSet;
import java.util.List;
/* /*
* Copyright (c) 2009 The Broad Institute * Copyright (c) 2009 The Broad Institute

4
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -95,11 +95,11 @@ public class PileupElement implements Comparable<PileupElement> {
// -------------------------------------------------------------------------- // --------------------------------------------------------------------------
public boolean isReducedRead() { public boolean isReducedRead() {
return ((GATKSAMRecord)read).isReducedRead(); return read.isReducedRead();
} }
public int getRepresentativeCount() { public int getRepresentativeCount() {
return isReducedRead() ? ((GATKSAMRecord)read).getReducedCount(offset) : 1; return isReducedRead() ? read.getReducedCount(offset) : 1;
} }
} }

2
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -243,7 +243,7 @@ public class ReadUtils {
public static GATKSAMRecord hardClipAdaptorSequence(final GATKSAMRecord read, int adaptorLength) { public static GATKSAMRecord hardClipAdaptorSequence(final GATKSAMRecord read, int adaptorLength) {
Pair<Integer, Integer> adaptorBoundaries = getAdaptorBoundaries(read, adaptorLength); Pair<Integer, Integer> adaptorBoundaries = getAdaptorBoundaries(read, adaptorLength);
GATKSAMRecord result = (GATKSAMRecord)read; GATKSAMRecord result = read;
if ( adaptorBoundaries != null ) { if ( adaptorBoundaries != null ) {
if ( read.getReadNegativeStrandFlag() && adaptorBoundaries.second >= read.getAlignmentStart() && adaptorBoundaries.first < read.getAlignmentEnd() ) if ( read.getReadNegativeStrandFlag() && adaptorBoundaries.second >= read.getAlignmentStart() && adaptorBoundaries.first < read.getAlignmentEnd() )