From ec83bc6ec55bc6f1cc0a648cd4120d16542f43ea Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 12 Oct 2009 21:11:13 +0000
Subject: [PATCH] This somehow didn't make it into subversion the last time.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1814 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/Recalibration/LocalMapType.java   | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/LocalMapType.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/LocalMapType.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/LocalMapType.java
new file mode 100755
index 000000000..9607b8226
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/LocalMapType.java
@@ -0,0 +1,34 @@
+package org.broadinstitute.sting.playground.gatk.walkers.Recalibration;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: Oct 9, 2009
+ * Time: 11:39:34 AM
+ * To change this template use File | Settings | File Templates.
+ */
+class LocalMapType {
+
+    public AlignmentContext context;
+    public ReferenceContext ref;
+    public RefMetaDataTracker tracker;
+
+    public LocalMapType(AlignmentContext context, ReferenceContext ref, RefMetaDataTracker tracker) {
+        this.context = context;
+        this.ref = ref;
+        this.tracker = tracker;
+    }
+
+    public int numReads() {
+        return context.numReads();
+    }
+
+    public int qScore(int read) {
+        return (int) context.getReads().get(read).getBaseQualities()[context.getOffsets().get(read)];
+    }
+
+}