From dc05b71e39b1e0124a5954a9c561d4556269117d Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Mon, 6 Feb 2012 11:10:24 -0500
Subject: [PATCH] Updating Covariate interface with Mauricio to include an
 errorModel parameter. On the fly recalibration of base insertion and base
 deletion quals is live for the HaplotypeCaller

---
 .../walkers/recalibration/ContextCovariate.java  |  5 +++--
 .../recalibration/CountCovariatesWalker.java     |  3 ++-
 .../gatk/walkers/recalibration/Covariate.java    | 10 ++++++----
 .../walkers/recalibration/CycleCovariate.java    |  3 ++-
 .../walkers/recalibration/DinucCovariate.java    | 11 ++++++-----
 .../recalibration/GCContentCovariate.java        |  3 ++-
 .../recalibration/HomopolymerCovariate.java      |  3 ++-
 .../recalibration/MappingQualityCovariate.java   |  3 ++-
 .../recalibration/MinimumNQSCovariate.java       |  3 ++-
 .../walkers/recalibration/PositionCovariate.java |  3 ++-
 .../recalibration/PrimerRoundCovariate.java      |  3 ++-
 .../recalibration/QualityScoreCovariate.java     | 16 ++++++++++++----
 .../recalibration/ReadGroupCovariate.java        |  5 +++--
 .../walkers/recalibration/RecalDataManager.java  |  5 +++--
 .../recalibration/TableRecalibrationWalker.java  |  3 ++-
 .../utils/recalibration/BaseRecalibration.java   |  4 ++--
 .../sting/utils/sam/GATKSAMRecord.java           |  5 +++--
 17 files changed, 56 insertions(+), 32 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ContextCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ContextCovariate.java
index 8b8f2cee9..0edd5d03b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ContextCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ContextCovariate.java
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 import java.util.Arrays;
 
@@ -35,7 +36,7 @@ import java.util.Arrays;
  * Date: 9/26/11
  */
 
-public class ContextCovariate implements Covariate {
+public class ContextCovariate implements ExperimentalCovariate {
 
     final int CONTEXT_SIZE = 8;
     String allN = "";
@@ -49,7 +50,7 @@ public class ContextCovariate implements Covariate {
     }
 
     @Override
-    public void getValues(SAMRecord read, Comparable[] comparable) {
+    public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
         byte[] bases = read.getReadBases();
         for(int i = 0; i < read.getReadLength(); i++) {
             comparable[i] = ( i-CONTEXT_SIZE < 0 ? allN : new String(Arrays.copyOfRange(bases,i-CONTEXT_SIZE,i)) );
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
index f6f05d39c..4e3d4048b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
@@ -41,6 +41,7 @@ import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
@@ -374,7 +375,7 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
 
                     RecalDataManager.parseColorSpace( gatkRead );
                     gatkRead.setTemporaryAttribute( COVARS_ATTRIBUTE,
-                            RecalDataManager.computeCovariates( gatkRead, requestedCovariates ));
+                            RecalDataManager.computeCovariates( gatkRead, requestedCovariates, BaseRecalibration.BaseRecalibrationType.BASE_SUBSTITUTION ));
                 }
 
                 // Skip this position if base quality is zero
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java
index 46ce006ee..2e32dbb8c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -32,7 +33,7 @@ import net.sf.samtools.SAMRecord;
  * User: rpoplin
  * Date: Oct 30, 2009
  *
- * The Covariate interface. A Covariate is a feature used in the recalibration that can be picked out of the read, offset, and corresponding reference bases
+ * The Covariate interface. A Covariate is a feature used in the recalibration that can be picked out of the read.
  * In general most error checking and adjustments to the data are done before the call to the covariates getValue methods in order to speed up the code.
  * This unfortunately muddies the code, but most of these corrections can be done per read while the covariates get called per base, resulting in a big speed up.
  */
@@ -40,9 +41,10 @@ import net.sf.samtools.SAMRecord;
 public interface Covariate {
     public void initialize( RecalibrationArgumentCollection RAC ); // Initialize any member variables using the command-line arguments passed to the walkers
     public Comparable getValue( String str ); // Used to get the covariate's value from input csv file in TableRecalibrationWalker
-    public void getValues( SAMRecord read, Comparable[] comparable ); //Takes an array of size (at least) read.getReadLength() and fills it with covariate
-        //values for each position in the read. This method was created as an optimization over calling getValue( read, offset ) for each offset and allows
-        //read-specific calculations to be done just once rather than for each offset.
+    public void getValues( SAMRecord read, Comparable[] comparable, BaseRecalibration.BaseRecalibrationType modelType );
+            //Takes an array of size (at least) read.getReadLength() and fills it with covariate
+            //values for each position in the read. This method was created as an optimization over calling getValue( read, offset ) for each offset and allows
+            //read-specific calculations to be done just once rather than for each offset.
 }
 
 interface RequiredCovariate extends Covariate {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
index e72b426d0..00490d898 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
@@ -4,6 +4,7 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.NGSPlatform;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.EnumSet;
@@ -65,7 +66,7 @@ public class CycleCovariate implements StandardCovariate {
 
     // Used to pick out the covariate's value from attributes of the read
     @Override
-    public void getValues(SAMRecord read, Comparable[] comparable) {
+    public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
 
         //-----------------------------
         // Illumina, Solid, PacBio, and Complete Genomics
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
index 90768fe90..e60b1f795 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 import java.util.HashMap;
 
@@ -65,7 +66,7 @@ public class DinucCovariate implements StandardCovariate {
      * Takes an array of size (at least) read.getReadLength() and fills it with the covariate values for each position in the read.
      */
     @Override
-    public void getValues( SAMRecord read, Comparable[] result ) {
+    public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
         final HashMap<Integer, Dinuc> dinucHashMapRef = this.dinucHashMap; //optimize access to dinucHashMap
         final int readLength = read.getReadLength();
         final boolean negativeStrand = read.getReadNegativeStrandFlag();
@@ -78,7 +79,7 @@ public class DinucCovariate implements StandardCovariate {
         if(negativeStrand) {
             bases = BaseUtils.simpleReverseComplement(bases); //this is NOT in-place
         }
-        result[0] = NO_DINUC; // No dinuc at the beginning of the read
+        comparable[0] = NO_DINUC; // No dinuc at the beginning of the read
 
         prevBase = bases[0];
         offset++;
@@ -87,16 +88,16 @@ public class DinucCovariate implements StandardCovariate {
              // previous base in the reference. This is done in part to be consistent with unmapped reads.
              base = bases[offset];
              if( BaseUtils.isRegularBase( prevBase ) ) {
-                 result[offset] = dinucHashMapRef.get( Dinuc.hashBytes( prevBase, base ) );
+                 comparable[offset] = dinucHashMapRef.get( Dinuc.hashBytes( prevBase, base ) );
              } else {
-                 result[offset] = NO_DINUC;
+                 comparable[offset] = NO_DINUC;
              }
 
              offset++;
              prevBase = base;
         }
         if(negativeStrand) {
-            reverse( result );
+            reverse( comparable );
         }
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/GCContentCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/GCContentCovariate.java
index 1a085d5c0..e4ff415fe 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/GCContentCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/GCContentCovariate.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 /*
  * Copyright (c) 2010 The Broad Institute
@@ -78,7 +79,7 @@ public class GCContentCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(SAMRecord read, Comparable[] comparable) {
+    public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
         for(int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
index a54f9597b..24cb98a8d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -92,7 +93,7 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(SAMRecord read, Comparable[] comparable) {
+    public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
         for(int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java
index ad6484428..ec5b357a4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -54,7 +55,7 @@ public class MappingQualityCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(SAMRecord read, Comparable[] comparable) {
+    public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
         for(int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java
index 0c1c66a5f..21fd14e0c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -63,7 +64,7 @@ public class MinimumNQSCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(SAMRecord read, Comparable[] comparable) {
+    public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
         for(int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java
index 2a4497b0d..5c410ce5f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -53,7 +54,7 @@ public class PositionCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(SAMRecord read, Comparable[] comparable) {
+    public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
         for(int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java
index 4a9629234..e6aa44226 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -59,7 +60,7 @@ public class PrimerRoundCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(SAMRecord read, Comparable[] comparable) {
+    public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
         for(int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java
index de6d5065b..f85b52350 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java
@@ -1,6 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
+
+import java.util.Arrays;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -43,10 +46,15 @@ public class QualityScoreCovariate implements RequiredCovariate {
     }
 
     @Override
-    public void getValues(SAMRecord read, Comparable[] comparable) {
-        byte[] baseQualities = read.getBaseQualities();
-        for(int i = 0; i < read.getReadLength(); i++) {
-            comparable[i] = (int) baseQualities[i];
+    public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
+        if( modelType == BaseRecalibration.BaseRecalibrationType.BASE_SUBSTITUTION ) {
+            byte[] baseQualities = read.getBaseQualities();
+            for(int i = 0; i < read.getReadLength(); i++) {
+                comparable[i] = (int) baseQualities[i];
+            }
+        } else { // model == BASE_INSERTION || model == BASE_DELETION
+            Arrays.fill(comparable, 45); // Some day in the future when base insertion and base deletion quals exist the samtools API will
+                                         // be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45
         }
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java
index cb108feb8..e27077128 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -35,7 +36,7 @@ import net.sf.samtools.SAMRecord;
  * The Read Group covariate.
  */
 
-public class ReadGroupCovariate implements RequiredCovariate{
+public class ReadGroupCovariate implements RequiredCovariate {
 
     public static final String defaultReadGroup = "DefaultReadGroup";
 
@@ -45,7 +46,7 @@ public class ReadGroupCovariate implements RequiredCovariate{
     }
 
     @Override
-    public void getValues(SAMRecord read, Comparable[] comparable) {
+    public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
         final String readGroupId = read.getReadGroup().getReadGroupId();
         for(int i = 0; i < read.getReadLength(); i++) {
             comparable[i] = readGroupId;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index 66ad1fb9c..be02063de 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -571,7 +572,7 @@ public class RecalDataManager {
      * value for the ith position in the read and the jth covariate in
      * reqeustedCovariates list.
      */
-     public static Comparable[][] computeCovariates(final GATKSAMRecord gatkRead, final List<Covariate> requestedCovariates) {
+     public static Comparable[][] computeCovariates( final GATKSAMRecord gatkRead, final List<Covariate> requestedCovariates, final BaseRecalibration.BaseRecalibrationType modelType ) {
          //compute all covariates for this read
          final List<Covariate> requestedCovariatesRef = requestedCovariates;
          final int numRequestedCovariates = requestedCovariatesRef.size();
@@ -582,7 +583,7 @@ public class RecalDataManager {
 
          // Loop through the list of requested covariates and compute the values of each covariate for all positions in this read
          for( int i = 0; i < numRequestedCovariates; i++ ) {
-             requestedCovariatesRef.get(i).getValues( gatkRead, tempCovariateValuesHolder );
+             requestedCovariatesRef.get(i).getValues( gatkRead, tempCovariateValuesHolder, modelType );
              for(int j = 0; j < readLength; j++) {
                  //copy values into a 2D array that allows all covar types to be extracted at once for
                  //an offset j by doing covariateValues_offset_x_covar[j]. This avoids the need to later iterate over covar types.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index a569aefd2..a8006d506 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.text.XReadLines;
@@ -398,7 +399,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
         //compute all covariate values for this read
         final Comparable[][] covariateValues_offset_x_covar =
-            RecalDataManager.computeCovariates(read, requestedCovariates);
+            RecalDataManager.computeCovariates(read, requestedCovariates, BaseRecalibration.BaseRecalibrationType.BASE_SUBSTITUTION);
 
         // For each base in the read
         for( int offset = 0; offset < read.getReadLength(); offset++ ) {
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 2e785043d..ce52f09a2 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
@@ -177,13 +177,13 @@ public class BaseRecalibration {
         dataManager.addToAllTables( key, datum, QualityUtils.MIN_USABLE_Q_SCORE ); //BUGBUG: used to be Q5 now is Q6, probably doesn't matter
     }
     
-    public byte[] recalibrateRead( final GATKSAMRecord read, final byte[] originalQuals ) {
+    public byte[] recalibrateRead( final GATKSAMRecord read, final byte[] originalQuals, final BaseRecalibrationType modelType ) {
 
         final byte[] recalQuals = originalQuals.clone();
         
         //compute all covariate values for this read
         final Comparable[][] covariateValues_offset_x_covar =
-                RecalDataManager.computeCovariates(read, requestedCovariates);
+                RecalDataManager.computeCovariates(read, requestedCovariates, modelType);
     
         // For each base in the read
         for( int offset = 0; offset < read.getReadLength(); offset++ ) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index 66e957a41..bdcf2b210 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.utils.sam;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.NGSPlatform;
+import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 import java.util.Arrays;
 import java.util.HashMap;
@@ -194,7 +195,7 @@ public class GATKSAMRecord extends BAMRecord {
             // if the recal data was populated in the engine then recalibrate the quality scores on the fly
             // else give default values which are flat Q45
             if( GenomeAnalysisEngine.hasBaseRecalibration() ) {
-                quals = GenomeAnalysisEngine.getBaseRecalibration().recalibrateRead( this, quals ); // the original quals here are the flat base insertion/deletion quals, NOT the original base qualities
+                quals = GenomeAnalysisEngine.getBaseRecalibration().recalibrateRead( this, quals, BaseRecalibration.BaseRecalibrationType.BASE_INSERTION ); // the original quals here are the flat base insertion/deletion quals, NOT the original base qualities
             }
             // add the qual array to the read so that we don't have to do the recalibration work again
             setAttribute( BQSR_BASE_INSERTION_QUALITIES, quals );
@@ -210,7 +211,7 @@ public class GATKSAMRecord extends BAMRecord {
             // if the recal data was populated in the engine then recalibrate the quality scores on the fly
             // else give default values which are flat Q45
             if( GenomeAnalysisEngine.hasBaseRecalibration() ) {
-                quals = GenomeAnalysisEngine.getBaseRecalibration().recalibrateRead( this, quals ); // the original quals here are the flat base insertion/deletion quals, NOT the original base qualities
+                quals = GenomeAnalysisEngine.getBaseRecalibration().recalibrateRead( this, quals, BaseRecalibration.BaseRecalibrationType.BASE_DELETION ); // the original quals here are the flat base insertion/deletion quals, NOT the original base qualities
             }
             // add the qual array to the read so that we don't have to do the recalibration work again
             setAttribute( BQSR_BASE_DELETION_QUALITIES, quals );