diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java index e10334a77..6b4fec04e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java @@ -6,9 +6,7 @@ import org.broadinstitute.sting.utils.NGSPlatform; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import java.util.Arrays; import java.util.EnumSet; -import java.util.List; /* * Copyright (c) 2009 The Broad Institute diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java index daf6606ef..bab20b9e8 100755 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java @@ -95,11 +95,11 @@ public class PileupElement implements Comparable { // -------------------------------------------------------------------------- public boolean isReducedRead() { - return ((GATKSAMRecord)read).isReducedRead(); + return read.isReducedRead(); } public int getRepresentativeCount() { - return isReducedRead() ? ((GATKSAMRecord)read).getReducedCount(offset) : 1; + return isReducedRead() ? read.getReducedCount(offset) : 1; } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index e125b8c80..8d9018045 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -243,7 +243,7 @@ public class ReadUtils { public static GATKSAMRecord hardClipAdaptorSequence(final GATKSAMRecord read, int adaptorLength) { Pair adaptorBoundaries = getAdaptorBoundaries(read, adaptorLength); - GATKSAMRecord result = (GATKSAMRecord)read; + GATKSAMRecord result = read; if ( adaptorBoundaries != null ) { if ( read.getReadNegativeStrandFlag() && adaptorBoundaries.second >= read.getAlignmentStart() && adaptorBoundaries.first < read.getAlignmentEnd() )