From fe19539188fc8139e8773f9dae156fe15a3448a2 Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 27 Aug 2010 20:37:27 +0000
Subject: [PATCH] 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
---
 .../oneoffprojects/walkers/IndelConsistencyReadCounter.java  | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
index abff66830..f0a7e0ad6 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
+++ b/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++;
         }