From 486712bfc2f69d356da739098b8710142fe1bf47 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 1 Mar 2012 17:55:28 -0500
Subject: [PATCH] ugly RG encoding

---
 .../gatk/walkers/bqsr/ReadGroupCovariate.java | 22 +++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java
index 6076a7a20..aecdd3d4b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.Arrays;
+import java.util.HashMap;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -38,6 +39,10 @@ import java.util.Arrays;
  */
 
 public class ReadGroupCovariate implements RequiredCovariate {
+    
+    private final HashMap<String, Short> readGroupLookupTable = new HashMap<String, Short>();
+    private final HashMap<Short, String> readGroupReverseLookupTable = new HashMap<Short, String>();
+    private short nextId = 0;
 
     // Initialize any member variables using the command-line arguments passed to the walkers
     @Override
@@ -48,8 +53,17 @@ public class ReadGroupCovariate implements RequiredCovariate {
     public CovariateValues getValues(final GATKSAMRecord read) {
         final int l = read.getReadLength();
         final String readGroupId = read.getReadGroup().getReadGroupId();
-        String [] readGroups = new String[l];
-        Arrays.fill(readGroups, readGroupId);
+        short shortId;
+        if (readGroupLookupTable.containsKey(readGroupId)) 
+            shortId = readGroupLookupTable.get(readGroupId);
+        else {
+            shortId = nextId;
+            readGroupLookupTable.put(readGroupId, nextId);
+            readGroupReverseLookupTable.put(nextId, readGroupId);
+            nextId++;
+        }
+        Short [] readGroups = new Short[l];
+        Arrays.fill(readGroups, shortId);
         return new CovariateValues(readGroups, readGroups, readGroups);
     }
 
@@ -58,6 +72,10 @@ public class ReadGroupCovariate implements RequiredCovariate {
     public final Object getValue(final String str) {
         return str;
     }
+    
+    public final String decodeReadGroup(final short id) {
+        return readGroupReverseLookupTable.get(id);
+    }
 }