diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
index 368cb3d11..2226c6458 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
@@ -346,7 +346,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
 
         @Override
         protected String getFreezeFields() {
-            return String.format("if (num_threads.isDefined) nCoresRequest = num_threads%n");
+            return String.format("if (num_threads.isDefined) nCoresRequest = num_threads%nif (num_cpu_threads_per_data_thread.isDefined) nCoresRequest = Some(nCoresRequest.getOrElse(1) * num_cpu_threads_per_data_thread.getOrElse(1))%n");
         }
     }
 
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 2f9387acb..5d4020a07 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
@@ -61,17 +61,6 @@ public class BaseRecalibration {
 //            qualityScoreByFullCovariateKey[i] = new NestedHashMap();
 //    }
 
-    /**
-     * Thread local cache to allow multi-threaded use of this class
-     */
-    private ThreadLocal<ReadCovariates> readCovariatesCache;
-    {
-        readCovariatesCache = new ThreadLocal<ReadCovariates> () {
-            @Override protected ReadCovariates initialValue() {
-                return new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
-            }
-        };
-    }
 
     /**
      * Constructor using a GATK Report file
@@ -113,16 +102,7 @@ public class BaseRecalibration {
             }
         }
 
-        // Compute all covariates for the read
-        // TODO -- the need to clear here suggests there's an error in the indexing / assumption code
-        // TODO -- for BI and DI. Perhaps due to the indel buffer size on the ends of the reads?
-        // TODO -- the output varies depending on whether we clear or not
-        //final ReadCovariates readCovariates = readCovariatesCache.get().clear();
-
-        // the original code -- doesn't do any clearing
-        final ReadCovariates readCovariates = readCovariatesCache.get();
-
-        RecalUtils.computeCovariates(read, requestedCovariates, readCovariates);
+        final ReadCovariates readCovariates = RecalUtils.computeCovariates(read, requestedCovariates);
 
         for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
             if (disableIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {