From 65d0675a4e972c044414400f83b371189ec82c91 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 9 Jun 2009 01:01:13 +0000
Subject: [PATCH] Some changes regarding what to do when a cycle is completely
 busted.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@946 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/secondarybase/BasecallingReadModel.java              | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/secondarybase/BasecallingReadModel.java b/java/src/org/broadinstitute/sting/secondarybase/BasecallingReadModel.java
index 01c726efa..66de68317 100644
--- a/java/src/org/broadinstitute/sting/secondarybase/BasecallingReadModel.java
+++ b/java/src/org/broadinstitute/sting/secondarybase/BasecallingReadModel.java
@@ -232,6 +232,9 @@ public class BasecallingReadModel {
         int actualBasePrevIndex = (correctForContext && cycle > 0) ? BaseUtils.simpleBaseToBaseIndex(basePrev) : 0;
         int actualBaseCurIndex = BaseUtils.simpleBaseToBaseIndex(baseCur);
 
+        if (actualBasePrevIndex == -1) { actualBasePrevIndex = BaseUtils.getRandomBaseIndex(); }
+        if (actualBaseCurIndex == -1) { actualBaseCurIndex = BaseUtils.getRandomBaseIndex(); }
+
         double residualTheories = (double) (dist.length*dist[0].length - 1);
 
         for (int basePrevIndex = 0; basePrevIndex < dist.length; basePrevIndex++) {