diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRKeyManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRKeyManager.java
index cdd186e9f..c1449c5b3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRKeyManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRKeyManager.java
@@ -98,7 +98,7 @@ public class BQSRKeyManager {
      * @return one key in bitset representation per covariate
      */
     public List<BitSet> bitSetsFromAllKeys(BitSet[] allKeys, EventType eventType) {
-        List<BitSet> allBitSets = new LinkedList<BitSet>();                                                             // Generate one key per optional covariate
+        List<BitSet> allBitSets = new ArrayList<BitSet>();                                                              // Generate one key per optional covariate
 
         BitSet eventBitSet = BitSetUtils.bitSetFrom(eventType.index);                                                   // create a bitset with the event type
         int eventTypeBitIndex = nRequiredBits + nOptionalBits + nOptionalIDBits;                                        // Location in the bit set to add the event type bits
diff --git a/public/java/src/org/broadinstitute/sting/utils/BitSetUtils.java b/public/java/src/org/broadinstitute/sting/utils/BitSetUtils.java
index 98c901bcd..41889e2f5 100644
--- a/public/java/src/org/broadinstitute/sting/utils/BitSetUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/BitSetUtils.java
@@ -82,7 +82,7 @@ public class BitSetUtils {
      * @return a bitset representation of the integer
      */
     public static BitSet bitSetFrom(long number, int nBits) {
-        BitSet bitSet = new BitSet();
+        BitSet bitSet = new BitSet(nBits);
         boolean isNegative = number < 0;
         int bitIndex = 0;
         while (number != 0) {