Yuck - Picard's SAMRecord Comparator only deals with mapped reads. Adding an extended version that works for all reads.

After adding some more minor changes to the new realigner it now gets the same exact results as the original version - except that sometimes it doesn't clean when it shouldn't!
More testing coming.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2731 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java

@@ -206,7 +206,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             emit(readsNotToClean);
         }
 
-        writer.close();
+        if ( writer != null )
+            writer.close();
 
         if ( OUT_INDELS != null ) {
             try {

java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java

@@ -0,0 +1,56 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2009 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.gatk.walkers.indels;
+
+import net.sf.samtools.*;
+
+/**
+ * Extends Picard's Comparator for sorting SAMRecords by coordinate.  This one actually deals with unmapped reads
+ * (among other things) sitting at the same position as their mates (so that they both can be put into the same set).
+ */
+public class SAMRecordCoordinateComparatorWithUnmappedReads extends SAMRecordCoordinateComparator {
+    public int compare(final SAMRecord samRecord1, final SAMRecord samRecord2) {
+        int cmp = fileOrderCompare(samRecord1, samRecord2);
+        if ( cmp != 0 )
+            return cmp;
+
+        // deal with unmapped reads
+        if ( samRecord1.getReadUnmappedFlag() != samRecord2.getReadUnmappedFlag() )
+            return (samRecord1.getReadUnmappedFlag()? 1: -1);        
+
+        if ( samRecord1.getReadNegativeStrandFlag() != samRecord2.getReadNegativeStrandFlag() )
+            return (samRecord1.getReadNegativeStrandFlag()? 1: -1);
+
+        // even the names can be the same
+        cmp = samRecord1.getReadName().compareTo(samRecord2.getReadName());
+        if ( cmp != 0 )
+            return cmp;
+
+        if ( samRecord1.getDuplicateReadFlag() != samRecord2.getDuplicateReadFlag() )
+            return (samRecord1.getDuplicateReadFlag()? -1: 1);
+
+        // such a case was actually observed
+        return samRecord1.getMappingQuality() - samRecord2.getMappingQuality();
+    }
+}

java/src/org/broadinstitute/sting/gatk/walkers/indels/SortingSAMFileWriter.java

@@ -23,7 +23,7 @@ public class SortingSAMFileWriter implements SAMFileWriter {
     private int window;
 
     // the reads we are accumulating
-    private TreeSet<SAMRecord> cachedReads = new TreeSet<SAMRecord>(new SAMRecordCoordinateComparator());
+    private TreeSet<SAMRecord> cachedReads = new TreeSet<SAMRecord>(new SAMRecordCoordinateComparatorWithUnmappedReads());
 
 
     /**