From fea625632f0729fea1ead3340e0fffa9fca6b696 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 11 Jun 2012 15:45:58 -0400
Subject: [PATCH] Don't use asList because it maintains an iterator to the
 original list and then the result can't be used to create a new one

---
 .../sting/gatk/walkers/bqsr/RecalDataManager.java            | 5 +++--
 .../sting/utils/recalibration/BaseRecalibration.java         | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java
index d916abaae..f4c7873f4 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java
@@ -364,8 +364,9 @@ public class RecalDataManager {
 
             if (keyManager.getOptionalCovariates().size() > 0) {                                                        // initialize with the 'all covariates' table
                 // create a key manager for the delta table
-                List<Covariate> requiredCovariates = keyManager.getRequiredCovariates().subList(0, 1);                  // include the read group covariate as the only required covariate
-                List<Covariate> optionalCovariates = keyManager.getRequiredCovariates().subList(1, 2);                  // include the quality score covariate as an optional covariate
+                final List<Covariate> requiredCovariates = Arrays.asList(keyManager.getRequiredCovariates().get(0));    // include the read group covariate as the only required covariate
+                List<Covariate> optionalCovariates = new ArrayList<Covariate>();
+                optionalCovariates.add(keyManager.getRequiredCovariates().get(1));                                      // include the quality score covariate as an optional covariate
                 optionalCovariates.addAll(keyManager.getOptionalCovariates());                                          // include all optional covariates
                 deltaKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);                           // initialize the key manager
             }
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
index 5b5f99b3f..137ed1256 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
@@ -44,7 +44,7 @@ import java.util.*;
 public class BaseRecalibration {
     private QuantizationInfo quantizationInfo;                                                                          // histogram containing the map for qual quantization (calculated after recalibration is done)
     private LinkedHashMap<BQSRKeyManager, Map<BitSet, RecalDatum>> keysAndTablesMap;                                    // quick access reference to the read group table and its key manager
-    private ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>();                                      // list of all covariates to be used in this calculation
+    private ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>();                                              // list of all covariates to be used in this calculation
 
 
     /**