Resolving merge conflicts

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java

@@ -63,7 +63,7 @@ import java.util.TreeSet;
  */
 public class CompressionStash extends TreeSet<FinishedGenomeLoc> {
     public CompressionStash() {
-        super(new GenomeLocComparator());
+        super();
     }
 
     /**

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java

@@ -64,7 +64,6 @@ import org.broadinstitute.sting.gatk.walkers.PartitionType;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocComparator;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -267,8 +266,8 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
     public void initialize() {
         super.initialize();
         GenomeAnalysisEngine toolkit = getToolkit();
-        readNameHash = new HashMap<String, Long>();                         // prepare the read name hash to keep track of what reads have had their read names compressed
+        readNameHash = new HashMap<String, Long>();           // prepare the read name hash to keep track of what reads have had their read names compressed
-        intervalList = new TreeSet<GenomeLoc>(new GenomeLocComparator());   // get the interval list from the engine. If no interval list was provided, the walker will work in WGS mode
+        intervalList = new TreeSet<GenomeLoc>();              // get the interval list from the engine. If no interval list was provided, the walker will work in WGS mode
 
         if (toolkit.getIntervals() != null)
             intervalList.addAll(toolkit.getIntervals());

public/java/src/org/broadinstitute/sting/utils/GenomeLocComparator.java

@@ -1,81 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.sting.utils;
-
-import com.google.java.contract.Ensures;
-import com.google.java.contract.Requires;
-
-import java.util.Comparator;
-
-/**
- *
- * @author Mauricio Carneiro
- * @since 9/28/11
- */
-public class GenomeLocComparator implements Comparator<GenomeLoc> {
-    /**
-     * compares genomeLoc's contigs
-     *
-     * @param gl1 the genome loc to compare contigs
-     * @param gl2 the genome loc to compare contigs
-     * @return 0 if equal, -1 if gl2.contig is greater, 1 if gl1.contig is greater
-     */
-    @Requires("gl2 != null")
-    @Ensures("result == 0 || result == 1 || result == -1")
-    public final int compareContigs( GenomeLoc gl1, GenomeLoc gl2 ) {
-        if (gl1.contigIndex == gl2.contigIndex)
-            return 0;
-        else if (gl1.contigIndex > gl2.contigIndex)
-            return 1;
-        return -1;
-    }
-
-    @Requires("gl2 != null")
-    @Ensures("result == 0 || result == 1 || result == -1")
-    public int compare ( GenomeLoc gl1, GenomeLoc gl2 ) {
-        int result = 0;
-
-        if ( gl1 == gl2 ) {
-            result = 0;
-        }
-        else if(GenomeLoc.isUnmapped(gl1))
-            result = 1;
-        else if(GenomeLoc.isUnmapped(gl2))
-            result = -1;
-        else {
-            final int cmpContig = compareContigs(gl1, gl2);
-
-            if ( cmpContig != 0 ) {
-                result = cmpContig;
-            } else {
-                if ( gl1.getStart() < gl2.getStart() ) result = -1;
-                if ( gl1.getStart() > gl2.getStart() ) result = 1;
-            }
-        }
-
-        return result;
-    }
-}