From 08fab49d303bb6e9553d8c14daab5d024aa15564 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 6 Apr 2012 15:56:01 -0400
Subject: [PATCH] Added function to get bases from the current base forward in
 the window in ReferenceContext

---
 build.xml                                              |  4 ++--
 .../sting/gatk/contexts/ReferenceContext.java          | 10 ++++++++++
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/build.xml b/build.xml
index 8e9de2272..9a66d4699 100644
--- a/build.xml
+++ b/build.xml
@@ -955,8 +955,8 @@
                 <jvmarg value="-Dpipeline.run=${pipeline.run}" />
                 <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
                 <jvmarg line="${cofoja.jvm.args}"/>
-                <!-- <jvmarg value="-Xdebug"/> --> 
-                <!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5678"/> -->  
+<!--                 <jvmarg value="-Xdebug"/>  -->
+<!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/>   -->
 
                 <classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
                 <classfileset dir="${java.private.test.classes}" erroronmissingdir="false">
diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
index 376064cdb..1290319e2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
@@ -191,6 +191,16 @@ public class ReferenceContext {
         return basesCache;
     }
 
+    /**
+     * All the bases in the window from the current base forward to the end of the window.
+     */
+    public byte[] getForwardBases() {
+        final byte[] bases = getBases();
+        final int mid = locus.getStart() - window.getStart();
+        // todo -- warning of performance problem, especially if this is called over and over
+        return new String(bases).substring(mid).getBytes();
+    }
+
     @Deprecated
     public char getBaseAsChar() {
         return (char)getBase();