From 31d5df285993d68833f9358d077177b5e1aea65d Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 27 Oct 2009 15:58:20 +0000
Subject: [PATCH] Previous base now checks that the read matches the reference
 in the previous base window.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1915 348d0f76-0448-11de-a6fe-93d51630548a
---
 ...seTransitionTableCalculatorJavaWalker.java | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
index 61fe0509d..1abbc40e3 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
@@ -217,11 +217,30 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
             return false;
         } else if ( useSecondaryBase && read.getAttribute("SQ") == null )
             return false;
+        else if ( nPreviousBases >= 1 && previousReadBasesMismatchRef(read, offset, ref) )
+            return false;
         else {
             return true;
         }
     }
 
+    public boolean previousReadBasesMismatchRef( SAMRecord read, int offset, ReferenceContext ref ) {
+        int c = read.getReadNegativeStrandFlag() ? 1 : -1;
+        if ( offset + nPreviousBases*c < 0 ) {
+            return true;
+        } else if ( offset + nPreviousBases*c > read.getReadLength() ) {
+            return true;
+        }
+
+        for ( int prevBase = 1; prevBase <= nPreviousBases; prevBase ++ ) {
+            if ( Character.toUpperCase(read.getReadBases()[offset + prevBase*c]) != Character.toUpperCase(ref.getBases()[nPreviousBases+1+prevBase*c]) ) {
+                return true;
+            }
+        }
+
+        return false;
+    }
+
     public List<Comparable> buildConditions( SAMRecord read, int offset, ReferenceContext ref, ReadBackedPileup pileup ) {
         ArrayList<Comparable> conditions = new ArrayList<Comparable>();