From 12d6edfe7c282ca627b4feb9282079f22cfb41c3 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 30 Apr 2009 22:14:26 +0000
Subject: [PATCH] Only prints about first contig info setting

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@574 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/utils/GenomeLoc.java  | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index edc6910d7..6bed69ea5 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -74,7 +74,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
         	logger.info("Failed to load reference dictionary, falling back to lexicographic order for contigs");
             Utils.scareUser("Failed to load reference dictionary");
             return false;
-        }  else {
+        } else if ( contigInfo == null ){
             contigInfo = seqDict;
             logger.debug(String.format("Prepared reference sequence contig dictionary"));
             for (SAMSequenceRecord contig : seqDict.getSequences() ) {
@@ -450,6 +450,18 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
         n.incPos();
         return n;
     }
+
+    // Dangerous
+//    public boolean equals(Object o) {
+//        // Not strictly necessary, but often a good optimization
+//         if (this == o)
+//           return true;
+//         if (!(o instanceof GenomeLoc))
+//           return false;
+//         else
+//            return compareContigs((GenomeLoc)o) == 0;
+//    }
+
     //
     // Comparison operations
     //