From c7f22e410f5bfe6bbb3ea77187294787fdbc4939 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Thu, 9 Aug 2012 16:22:08 -0400 Subject: [PATCH] A few quick, minor findbugs fixes. --- .../sting/gatk/traversals/TraverseActiveRegions.java | 2 +- .../gatk/walkers/variantrecalibration/VariantDatum.java | 1 + public/java/src/org/broadinstitute/sting/utils/PairHMM.java | 2 +- .../org/broadinstitute/sting/utils/SWPairwiseAlignment.java | 6 +++--- .../sting/utils/activeregion/ActiveRegion.java | 4 ++-- .../sting/utils/activeregion/ActivityProfile.java | 3 --- 6 files changed, 8 insertions(+), 10 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java index 845c4eacf..979e0f2d6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java @@ -29,7 +29,7 @@ public class TraverseActiveRegions extends TraversalEngine workQueue = new LinkedList(); private final LinkedHashSet myReads = new LinkedHashSet(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java index 32350f0fa..a85129d78 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java @@ -52,6 +52,7 @@ public class VariantDatum implements Comparable { 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); } diff --git a/public/java/src/org/broadinstitute/sting/utils/PairHMM.java b/public/java/src/org/broadinstitute/sting/utils/PairHMM.java index 9fcb97a4d..ec4cf3386 100644 --- a/public/java/src/org/broadinstitute/sting/utils/PairHMM.java +++ b/public/java/src/org/broadinstitute/sting/utils/PairHMM.java @@ -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; diff --git a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java index 92d73a5ce..bc1158a4d 100755 --- a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java +++ b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java @@ -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) } /* ############################################## diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java index 18276f932..8e660350f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java @@ -90,11 +90,11 @@ public class ActiveRegion implements HasGenomeLocation, Comparable public void removeAll( final ArrayList 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; } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java index 7e736b7bf..73f3cc487 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java @@ -46,7 +46,6 @@ public class ActivityProfile { final boolean presetRegions; GenomeLoc regionStartLoc = null; final List 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;