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

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;