From 55f61b1f881d3441bc48452962a9b00de15a3181 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 3 Nov 2009 16:08:11 +0000
Subject: [PATCH] Bug fix in adjustment of the shift position.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1966 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelGenotyperV2Walker.java   | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
index 5929eea38..d57fcdebe 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
@@ -286,6 +286,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
             if ( DEBUG ) System.out.println("DEBUG>> indel observations present within "+NQS_WIDTH+" bases ahead. Resetting shift to "+request);
             attempts++;
             if ( attempts == 4 ) {
+                System.out.println("DEBUG>> attempts to preserve full NQS window failed; now trying to find any suitable position.") ;
                 failure = true;
                 break;
             }
@@ -297,14 +298,15 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
             // first position after the shift (this is bad for other reasons); if it breaks a nqs window, so be it
             request = initial_request;
             attempts = 0;
-            while ( tumor_context.hasIndelsInInterval(request,request) ||
-                  normal_context.hasIndelsInInterval(request,request) ) {
+            while ( tumor_context.hasIndelsInInterval(request,request+1) ||
+                  normal_context.hasIndelsInInterval(request,request+1) ) {
                 request--;
                 if ( DEBUG ) System.out.println("DEBUG>> indel observations present within "+NQS_WIDTH+" bases ahead. Resetting shift to "+request);
                 attempts++;
                 if ( attempts == 50 ) throw new StingException("Indel at every position in the interval ["+request+", "+initial_request+"]. Can not find a break to shift context window to");
             }
         }
+        if ( DEBUG ) System.out.println("DEBUG>> Found acceptable target position "+request);
         return request;
     }