From 277493dd8315f155c9ce4d49679a73316a397dc4 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 12 Jun 2012 15:56:09 -0400
Subject: [PATCH] Yet more instances of Lists changed over to native arrays

---
 .../sting/gatk/walkers/bqsr/RecalDataManager.java           | 6 +++---
 1 file changed, 3 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 5f4c94c78..bf4f223e4 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
@@ -611,13 +611,13 @@ public class RecalDataManager {
      * @param requestedCovariates The list of requested covariates.
      * @return a matrix with all the covariates calculated for every base in the read
      */
-    public static ReadCovariates computeCovariates(final GATKSAMRecord read, final List<Covariate> requestedCovariates) {
-        final int numRequestedCovariates = requestedCovariates.size();
+    public static ReadCovariates computeCovariates(final GATKSAMRecord read, final Covariate[] requestedCovariates) {
+        final int numRequestedCovariates = requestedCovariates.length;
         final int readLength = read.getReadLength();
         final ReadCovariates readCovariates = new ReadCovariates(readLength, numRequestedCovariates);
 
         // Loop through the list of requested covariates and compute the values of each covariate for all positions in this read
-        for (Covariate covariate : requestedCovariates)
+        for (final Covariate covariate : requestedCovariates)
             readCovariates.addCovariate(covariate.getValues(read));
 
         return readCovariates;