From a57500b2fceda91deff93a59182da460614a1a57 Mon Sep 17 00:00:00 2001
From: meganshand <mshand@broadinstitute.org>
Date: Tue, 29 Sep 2015 11:52:09 -0400
Subject: [PATCH] ROCCurve High Confidence Mode

Integration Tests

Updated test

Changed method

Minor changes

Changed whitespace

Fixed uncalled counts and 0 in R

Fixed ReadBackedPileUp

Removed imports and changed MD5

Fixed failing test

Adding vqslod color

Updating script to create KB

Fixing integration test now that the KB is bigger

Adressing comments
---
 .../src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java
index c913e6efd..d41072adb 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java
@@ -62,6 +62,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Serializable, HasGenome
     // TODO - WARNING WARNING WARNING code somehow depends on the name of the contig being null!
     public static final GenomeLoc UNMAPPED = new GenomeLoc((String)null);
     public static final GenomeLoc WHOLE_GENOME = new GenomeLoc("all");
+    public static final GenomeLoc END_OF_GENOME = new GenomeLoc("Y", 23, 59347566, 59347566);
 
     public static final boolean isUnmapped(GenomeLoc loc) {
         return loc == UNMAPPED;