From caedfed86067c2159b66c61e4748d37bb2358dd0 Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 4 Jan 2011 18:01:48 +0000
Subject: [PATCH] Fix bug where indels being incorrectly classified in
 VariantEval module

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4929 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/varianteval/IndelStatistics.java       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelStatistics.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelStatistics.java
index 34f0732da..12142bf96 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelStatistics.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelStatistics.java
@@ -337,7 +337,7 @@ public class IndelStatistics extends VariantEvaluator {
 
 
             // See first if indel is a repetition of bases before current
-            int indStart = refBases.length/2-eventLength;
+            int indStart = refBases.length/2-eventLength+1;
 
             boolean done = false;
             int numRepetitions = 0;
@@ -359,7 +359,7 @@ public class IndelStatistics extends VariantEvaluator {
 
             // now do it forward
             done = false;
-            indStart = refBases.length/2;
+            indStart = refBases.length/2+1;
             while (!done) {
                 if (indStart + eventLength >= refBases.length)
                     break;