From aef519b42704813ce1a67561e4ceb0a857ac0fc0 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 19 Jun 2009 16:46:05 +0000
Subject: [PATCH] more comparisons

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1059 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/ComparableSAMRecord.java      | 23 ++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/ComparableSAMRecord.java b/java/src/org/broadinstitute/sting/utils/ComparableSAMRecord.java
index 9e9716b5e..27540bb77 100755
--- a/java/src/org/broadinstitute/sting/utils/ComparableSAMRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/ComparableSAMRecord.java
@@ -5,9 +5,11 @@ import net.sf.samtools.SAMRecord;
 public class ComparableSAMRecord implements Comparable<ComparableSAMRecord> {
 
     private SAMRecord record;
+    private GenomeLoc loc;
 
     public ComparableSAMRecord(SAMRecord record) {
         this.record = record;
+        this.loc = new GenomeLoc(record);
     }
 
     public SAMRecord getRecord() {
@@ -16,13 +18,28 @@ public class ComparableSAMRecord implements Comparable<ComparableSAMRecord> {
 
     public int compareTo(ComparableSAMRecord o) {
         // first sort by start position
-        GenomeLoc myLoc = new GenomeLoc(record);
-        GenomeLoc hisLoc = new GenomeLoc(o.getRecord());
-        int comparison = myLoc.compareTo(hisLoc);
+        int comparison = loc.compareTo(o.loc);
         // if the reads have the same start position, we must give a non-zero comparison
         // (because java Sets often require "consistency with equals")
         if ( comparison == 0 )
             comparison = record.getReadName().compareTo(o.getRecord().getReadName());
+        // if the read names are the same, use the first of the pair if appropriate
+        if ( comparison == 0 )
+            comparison = ( record.getFirstOfPairFlag() ? -1 : 1);
         return comparison;
     }
+
+    public boolean equals(Object obj) {
+        if ( !(obj instanceof ComparableSAMRecord) )
+            return false;
+        if ( this == obj )
+            return true;
+
+        ComparableSAMRecord csr = (ComparableSAMRecord)obj;
+        if ( loc.compareTo(csr.loc) != 0 )
+            return false;
+        if ( !record.getReadName().equals(csr.getRecord().getReadName()) )
+            return false;
+        return ( record.getFirstOfPairFlag() == csr.record.getFirstOfPairFlag() );
+    }
 }
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