From d8cfd707bc13d1bd8a1234939fa83489d79173cc Mon Sep 17 00:00:00 2001
From: sjia <sjia@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 15 Dec 2009 20:35:18 +0000
Subject: [PATCH] Updated documentation

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2363 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../HLAcaller/FrequencyFileReader.java        | 21 +++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FrequencyFileReader.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FrequencyFileReader.java
index bd585a2ac..986c4cb26 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FrequencyFileReader.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FrequencyFileReader.java
@@ -1,6 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
+/**
+ * File reader used by other Walkers to read HLA allele frequencies.
  */
 
 package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
@@ -13,12 +12,16 @@ import java.util.Hashtable;
  */
 public class FrequencyFileReader {
     Hashtable AlleleFrequencies = new Hashtable();
+    Hashtable UniqueAlleles = new Hashtable();
 
     public Hashtable GetAlleleFrequencies(){
         return AlleleFrequencies;
     }
 
-    public void ReadFile(String filename){
+    public Hashtable GetUniqueAlleles(){
+        return UniqueAlleles;
+    }
+    public void ReadFile(String filename, String uniqueAllelesFile){
         try{
             FileInputStream fstream = new FileInputStream(filename);
             DataInputStream in = new DataInputStream(fstream);
@@ -31,6 +34,16 @@ public class FrequencyFileReader {
                 //System.out.printf("Loaded: %s\t%s\n",s[0],AlleleFrequencies.get(s[0]).toString());
             }
             in.close();
+
+            fstream = new FileInputStream(uniqueAllelesFile);
+            in = new DataInputStream(fstream);
+            br = new BufferedReader(new InputStreamReader(in));
+            //Read File Line By Line
+            while ((strLine = br.readLine()) != null)   {
+                UniqueAlleles.put(strLine,strLine);
+                //System.out.printf("Loaded: %s\t%s\n",s[0],AlleleFrequencies.get(s[0]).toString());
+            }
+            in.close();
         }catch (Exception e){//Catch exception if any
             System.err.println("FrequencyFileReader Error: " + e.getMessage());
         }