Small bug fix: if a read falls at the edge of an indel event (but is not part of it), don't count it towards consistency computation.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4152 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java

@@ -63,9 +63,12 @@ public class IndelConsistencyReadCounter extends ReadWalker<Integer, Integer> {
         }
 
         if ( indel != null ) {
+            if ( read.getAlignmentEnd() == indel.getStart() )
+                return 0;
+
             if ( !containsAnyIndel(read) || !containsIndel(read, indel) )
                 misalignedReads++;
-            else
+             else
                 consistentReads++;
         }