From c05451047c93ebc56cd022415cdc613114bb4e7e Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 18 Jul 2011 15:43:52 -0400
Subject: [PATCH] Support for multiple records at the same site.  The first
 record gets chr:start, and subsequent records get chr:start_2, chr:start_3,
 etc.

---
 .../sting/gatk/walkers/diffengine/VCFDiffableReader.java  | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
index df2a5cda1..77a992ce0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -72,13 +72,19 @@ public class VCFDiffableReader implements DiffableReader {
             }
 
             String line = lineReader.readLine();
-            int count = 0;
+            int count = 0, nRecordsAtPos = 1;
+            String prevName = "";
             while ( line != null ) {
                 if ( count++ > maxElementsToRead && maxElementsToRead != -1)
                     break;
 
                 VariantContext vc = (VariantContext)vcfCodec.decode(line);
                 String name = vc.getChr() + ":" + vc.getStart();
+                if ( name.equals(prevName) ) {
+                    name += "_" + ++nRecordsAtPos;
+                } else {
+                    prevName = name;
+                }
                 DiffNode vcRoot = DiffNode.empty(name, root);
 
                 // add fields