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A few quick, minor findbugs fixes.

This commit is contained in:
Ryan Poplin 2012-08-09 16:22:08 -04:00
parent e48727dae3
commit c7f22e410f
6 changed files with 8 additions and 10 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
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@ -29,7 +29,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
/**
* our log, which we want to capture anything from this class
*/
protected static Logger logger = Logger.getLogger(TraversalEngine.class);
protected final static Logger logger = Logger.getLogger(TraversalEngine.class);
private final LinkedList<org.broadinstitute.sting.utils.activeregion.ActiveRegion> workQueue = new LinkedList<org.broadinstitute.sting.utils.activeregion.ActiveRegion>();
private final LinkedHashSet<GATKSAMRecord> myReads = new LinkedHashSet<GATKSAMRecord>();

1
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
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@ -52,6 +52,7 @@ public class VariantDatum implements Comparable<VariantDatum> {
public int worstAnnotation;
public MultivariateGaussian assignment; // used in K-means implementation
@Override
public int compareTo( final VariantDatum other ) {
return Double.compare(this.lod, other.lod);
}

2
public/java/src/org/broadinstitute/sting/utils/PairHMM.java
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@ -36,7 +36,7 @@ import java.util.*;
*/
public class PairHMM {
private static final int MAX_CACHED_QUAL = (int)Byte.MAX_VALUE;
private static final int MAX_CACHED_QUAL = (int)Byte.MAX_VALUE - 1;
private static final byte DEFAULT_GOP = (byte) 45;
private static final byte DEFAULT_GCP = (byte) 10;
private static final double BANDING_TOLERANCE = 22.0;

6
public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
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@ -713,11 +713,11 @@ public class SWPairwiseAlignment {
System.err.println("Only one "+argname+" argument is allowed");
System.exit(1);
}
if ( l.get(0).equals("true") ) return new Boolean(true);
if ( l.get(0).equals("false") ) return new Boolean(false);
if ( l.get(0).equals("true") ) return Boolean.valueOf(true);
if ( l.get(0).equals("false") ) return Boolean.valueOf(false);
System.err.println("Can not parse value provided for "+argname+" argument ("+l.get(0)+"); true/false are allowed");
System.exit(1);
return null;
return Boolean.valueOf(false); // This value isn't used because it is preceded by System.exit(1)
}
/* ##############################################

4
public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
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@ -90,11 +90,11 @@ public class ActiveRegion implements HasGenomeLocation, Comparable<ActiveRegion>
public void removeAll( final ArrayList<GATKSAMRecord> readsToRemove ) { reads.removeAll( readsToRemove ); }
public boolean equalExceptReads(final ActiveRegion other) {
if ( ! activeRegionLoc.equals(other.activeRegionLoc) ) return false;
if ( activeRegionLoc.compareTo(other.activeRegionLoc) != 0 ) return false;
if ( isActive != other.isActive ) return false;
if ( genomeLocParser != other.genomeLocParser ) return false;
if ( extension != other.extension ) return false;
if ( ! extendedLoc.equals(other.extendedLoc) ) return false;
if ( extendedLoc.compareTo(other.extendedLoc) != 0 ) return false;
return true;
}
}

3
public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
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@ -46,7 +46,6 @@ public class ActivityProfile {
final boolean presetRegions;
GenomeLoc regionStartLoc = null;
final List<ActivityProfileResult> isActiveList;
private GenomeLoc lastLoc = null;
private static final int FILTER_SIZE = 80;
private static final double[] GaussianKernel;
@ -75,8 +74,6 @@ public class ActivityProfile {
public void add(final GenomeLoc loc, final ActivityProfileResult result) {
if ( loc.size() != 1 )
throw new ReviewedStingException("Bad add call to ActivityProfile: loc " + loc + " size != 1" );
if ( lastLoc != null && loc.getStart() != lastLoc.getStop() + 1 )
throw new ReviewedStingException("Bad add call to ActivityProfile: lastLoc added " + lastLoc + " and next is " + loc);
isActiveList.add(result);
if( regionStartLoc == null ) {
regionStartLoc = loc;