Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java

@@ -107,7 +107,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
                 }
 
                 // If this is the last pileup for this shard calculate the minimum alignment start so that we know 
-                //   which active regions in the work queue are now safe to process
+                // which active regions in the work queue are now safe to process
                 if( !locusView.hasNext() ) {
                     for( final PileupElement p : locus.getBasePileup() ) {
                         final GATKSAMRecord read = p.getRead();
@@ -135,7 +135,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
                 }
             }
 
-            // Since we've sufficiently past this point (or this contig!) in the workQueue we can unload those regions and process them
+            // Since we've traversed sufficiently past this point (or this contig!) in the workQueue we can unload those regions and process them
             while( workQueue.peek() != null && (workQueue.peek().getExtendedLoc().getStop() < minStart || !workQueue.peek().getExtendedLoc().getContig().equals(dataProvider.getLocus().getContig())) ) {
                 final ActiveRegion activeRegion = workQueue.remove();
                 sum = processActiveRegion( activeRegion, myReads, workQueue, sum, walker );
@@ -190,7 +190,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
         reads.removeAll( placedReads ); // remove all the reads which have been placed into their active region
 
         logger.debug(">> Map call with " + activeRegion.getReads().size() + " " + (activeRegion.isActive ? "active" : "inactive") + " reads @ " + activeRegion.getLocation() + " with full extent: " + activeRegion.getReferenceLoc());
-        final M x = walker.map( activeRegion, null ); // BUGBUG: tracker needs to be filled in and passed to the walker
+        final M x = walker.map( activeRegion, null );
         return walker.reduce( x, sum );
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java

@@ -5,14 +5,12 @@ import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.IntervalBinding;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.DuplicateReadFilter;
 import org.broadinstitute.sting.gatk.filters.FailsVendorQualityCheckFilter;
 import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentFilter;
 import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -77,7 +75,7 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
     public abstract double isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context);
 
     // Map over the ActiveRegion
-    public abstract MapType map(final ActiveRegion activeRegion, final ReadMetaDataTracker metaDataTracker);
+    public abstract MapType map(final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker);
 
     public final GenomeLocSortedSet extendIntervals( final GenomeLocSortedSet intervals, final GenomeLocParser genomeLocParser, IndexedFastaSequenceFile reference ) {
         final int activeRegionExtension = this.getClass().getAnnotation(ActiveRegionExtension.class).extension();

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java

@@ -22,8 +22,8 @@ import java.util.*;
  * User: chartl
  * Date: 9/14/11
  * Time: 12:24 PM
- * To change this template use File | Settings | File Templates.
  */
+
 public class MVLikelihoodRatio extends InfoFieldAnnotation implements ExperimentalAnnotation, RodRequiringAnnotation {
 
     private MendelianViolation mendelianViolation = null;

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java

@@ -98,4 +98,9 @@ public class ContextCovariate implements StandardCovariate {
         return s;
     }
 
+    // Used to get the covariate's value from input csv file during on-the-fly recalibration
+    @Override
+    public final Comparable getValue(final String str) {
+        return str;
+    }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java

@@ -53,6 +53,7 @@ public interface Covariate {
      */
     public CovariateValues getValues(GATKSAMRecord read);
 
+    public Comparable getValue(String str); // Used to get the covariate's value from input csv file during on-the-fly recalibration
 }
 
 interface RequiredCovariate extends Covariate {}

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CovariateKeySet.java

@@ -15,18 +15,18 @@ public class CovariateKeySet {
 
     private int nextCovariateIndex;
     
-    private final String mismatchesCovariateName = "M";
+    public final static String mismatchesCovariateName = "M";
-    private final String insertionsCovariateName = "I";
+    public final static String insertionsCovariateName = "I";
-    private final String  deletionsCovariateName = "D";
+    public final static String  deletionsCovariateName = "D";
 
     public CovariateKeySet(int readLength, int numberOfCovariates) {
         numberOfCovariates++;                                               // +1 because we are adding the mismatch covariate (to comply with the molten table format)
         this.mismatchesKeySet = new Object[readLength][numberOfCovariates]; 
         this.insertionsKeySet = new Object[readLength][numberOfCovariates];
         this.deletionsKeySet  = new Object[readLength][numberOfCovariates];
-        initializeCovariateKeySet(this.mismatchesKeySet, this.mismatchesCovariateName);
+        initializeCovariateKeySet(this.mismatchesKeySet, mismatchesCovariateName);
-        initializeCovariateKeySet(this.insertionsKeySet, this.insertionsCovariateName);
+        initializeCovariateKeySet(this.insertionsKeySet, insertionsCovariateName);
-        initializeCovariateKeySet(this.deletionsKeySet,  this.deletionsCovariateName);
+        initializeCovariateKeySet(this.deletionsKeySet,  deletionsCovariateName);
         this.nextCovariateIndex = 0;
     }
     

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java

@@ -196,4 +196,9 @@ public class CycleCovariate implements StandardCovariate {
         return new CovariateValues(cycles, cycles, cycles);
     }
 
+    // Used to get the covariate's value from input csv file during on-the-fly recalibration
+    @Override
+    public final Comparable getValue(final String str) {
+        return Integer.parseInt(str);
+    }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QualityScoreCovariate.java

@@ -39,39 +39,35 @@ import java.util.Arrays;
 
 public class QualityScoreCovariate implements RequiredCovariate {
 
-    private byte defaultMismatchesQuality;                                      // walker parameter. Must be > 0 to be used, otherwise we use the quality from the read.
-    private byte defaultInsertionsQuality;                                      // walker parameter. Must be > 0 to be used, otherwise we use the quality from the read.
-    private byte  defaultDeletionsQuality;                                      // walker parameter. Must be > 0 to be used, otherwise we use the quality from the read.
-        
     // Initialize any member variables using the command-line arguments passed to the walkers
     @Override
     public void initialize(final RecalibrationArgumentCollection RAC) {
-        defaultMismatchesQuality = RAC.MISMATCHES_DEFAULT_QUALITY;
-        defaultInsertionsQuality = RAC.INSERTIONS_DEFAULT_QUALITY;
-         defaultDeletionsQuality = RAC.DELETIONS_DEFAULT_QUALITY; 
     }
 
     @Override
     public CovariateValues getValues(final GATKSAMRecord read) {
         int readLength = read.getReadLength();
-        
+
-        Byte [] mismatches = new Byte[readLength];
+        Integer [] mismatches = new Integer[readLength];
-        Byte [] insertions = new Byte[readLength];
+        Integer [] insertions = new Integer[readLength];
-        Byte []  deletions = new Byte[readLength];
+        Integer []  deletions = new Integer[readLength];
-        
+
         byte [] baseQualities = read.getBaseQualities();
+        byte [] baseInsertionQualities = read.getBaseInsertionQualities();
+        byte [] baseDeletionQualities = read.getBaseDeletionQualities();
 
-        if (defaultMismatchesQuality >= 0)
+        for (int i=0; i<baseQualities.length; i++) {
-            Arrays.fill(mismatches, defaultMismatchesQuality);                  // if the user decides to override the base qualities in the read, use the flat value
+            mismatches[i] = (int) baseQualities[i];
-        else {
+            insertions[i] = (int) baseInsertionQualities[i];
-            for (int i=0; i<baseQualities.length; i++)
+            deletions[i] = (int) baseDeletionQualities[i];
-                mismatches[i] = baseQualities[i];
         }
 
-        Arrays.fill(insertions, defaultInsertionsQuality);                      // Some day in the future when base insertion and base deletion quals exist the samtools API will
-        Arrays.fill( deletions, defaultDeletionsQuality);                       // be updated and the original quals will be pulled here, but for now we assume the original quality is a flat value (parameter)
-
         return new CovariateValues(mismatches, insertions, deletions);
     }
 
+    // Used to get the covariate's value from input csv file during on-the-fly recalibration
+    @Override
+    public final Comparable getValue(final String str) {
+        return Integer.parseInt(str);
+    }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java

@@ -52,6 +52,12 @@ public class ReadGroupCovariate implements RequiredCovariate {
         Arrays.fill(readGroups, readGroupId);
         return new CovariateValues(readGroups, readGroups, readGroups);
     }
+
+    // Used to get the covariate's value from input csv file during on-the-fly recalibration
+    @Override
+    public final Comparable getValue(final String str) {
+        return str;
+    }
 }
 
 

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java

@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -52,20 +53,23 @@ import java.util.Map;
  */
 
 public class RecalDataManager {
-    public final NestedHashMap nestedHashMap;                           // The full dataset
+    public final NestedHashMap nestedHashMap;                                                           // The full dataset
-    private final NestedHashMap dataCollapsedReadGroup;                 // Table where everything except read group has been collapsed
+    private final HashMap<BaseRecalibrationType, NestedHashMap> dataCollapsedReadGroup;                 // Table where everything except read group has been collapsed
-    private final NestedHashMap dataCollapsedQualityScore;              // Table where everything except read group and quality score has been collapsed
+    private final HashMap<BaseRecalibrationType, NestedHashMap> dataCollapsedQualityScore;              // Table where everything except read group and quality score has been collapsed
-    private final ArrayList<NestedHashMap> dataCollapsedByCovariate;    // Tables where everything except read group, quality score, and given covariate has been collapsed
+    private final HashMap<BaseRecalibrationType, ArrayList<NestedHashMap>> dataCollapsedByCovariate;    // Tables where everything except read group, quality score, and given covariate has been collapsed
 
-    public final static String ORIGINAL_QUAL_ATTRIBUTE_TAG = "OQ";      // The tag that holds the original quality scores
     public final static String COLOR_SPACE_QUAL_ATTRIBUTE_TAG = "CQ";   // The tag that holds the color space quality scores for SOLID bams
     public final static String COLOR_SPACE_ATTRIBUTE_TAG = "CS";        // The tag that holds the color space for SOLID bams
     public final static String COLOR_SPACE_INCONSISTENCY_TAG = "ZC";    // A new tag made up for the recalibrator which will hold an array of ints which say if this base is inconsistent with its color
-    private static boolean warnUserNullReadGroup = false;
     private static boolean warnUserNullPlatform = false;
 
     private static final String COVARS_ATTRIBUTE = "COVARS";                   // used to store covariates array as a temporary attribute inside GATKSAMRecord.\
 
+    public enum BaseRecalibrationType {
+        BASE_SUBSTITUTION,
+        BASE_INSERTION,
+        BASE_DELETION
+    }
 
     public enum SOLID_RECAL_MODE {
         /**
@@ -109,13 +113,18 @@ public class RecalDataManager {
     }
 
     public RecalDataManager(final boolean createCollapsedTables, final int numCovariates) {
-        if (createCollapsedTables) { // Initialize all the collapsed tables, only used by TableRecalibrationWalker
+        if (createCollapsedTables) { // Initialize all the collapsed tables, only used by on-the-fly recalibration
             nestedHashMap = null;
-            dataCollapsedReadGroup = new NestedHashMap();
+            dataCollapsedReadGroup = new HashMap<BaseRecalibrationType, NestedHashMap>();
-            dataCollapsedQualityScore = new NestedHashMap();
+            dataCollapsedQualityScore = new HashMap<BaseRecalibrationType, NestedHashMap>();
-            dataCollapsedByCovariate = new ArrayList<NestedHashMap>();
+            dataCollapsedByCovariate = new HashMap<BaseRecalibrationType, ArrayList<NestedHashMap>>();
-            for (int iii = 0; iii < numCovariates - 2; iii++) { // readGroup and QualityScore aren't counted here, their tables are separate
+            for ( final BaseRecalibrationType errorModel : BaseRecalibrationType.values() ) {
-                dataCollapsedByCovariate.add(new NestedHashMap());
+                dataCollapsedReadGroup.put(errorModel, new NestedHashMap());
+                dataCollapsedQualityScore.put(errorModel, new NestedHashMap());
+                dataCollapsedByCovariate.put(errorModel, new ArrayList<NestedHashMap>());
+                for (int iii = 0; iii < numCovariates - 2; iii++) { // readGroup and QualityScore aren't counted here, their tables are separate
+                    dataCollapsedByCovariate.get(errorModel).add(new NestedHashMap());
+                }
             }
         }
         else {
@@ -137,7 +146,7 @@ public class RecalDataManager {
      * @param fullDatum                  The RecalDatum which is the data for this mapping
      * @param PRESERVE_QSCORES_LESS_THAN The threshold in report quality for adding to the aggregate collapsed table
      */
-    public final void addToAllTables(final Object[] key, final RecalDatum fullDatum, final int PRESERVE_QSCORES_LESS_THAN) {
+    public final void addToAllTables(final Object[] key, final RecalDatum fullDatum, final int PRESERVE_QSCORES_LESS_THAN, final BaseRecalibrationType errorModel ) {
 
         // The full dataset isn't actually ever used for anything because of the sequential calculation so no need to keep the full data HashMap around
         //data.put(key, thisDatum); // add the mapping to the main table
@@ -151,9 +160,9 @@ public class RecalDataManager {
         // Create dataCollapsedReadGroup, the table where everything except read group has been collapsed
         if (qualityScore >= PRESERVE_QSCORES_LESS_THAN) {
             readGroupCollapsedKey[0] = key[0]; // Make a new key with just the read group
-            collapsedDatum = (RecalDatum) dataCollapsedReadGroup.get(readGroupCollapsedKey);
+            collapsedDatum = (RecalDatum) dataCollapsedReadGroup.get(errorModel).get(readGroupCollapsedKey);
             if (collapsedDatum == null) {
-                dataCollapsedReadGroup.put(new RecalDatum(fullDatum), readGroupCollapsedKey);
+                dataCollapsedReadGroup.get(errorModel).put(new RecalDatum(fullDatum), readGroupCollapsedKey);
             }
             else {
                 collapsedDatum.combine(fullDatum); // using combine instead of increment in order to calculate overall aggregateQReported
@@ -163,24 +172,24 @@ public class RecalDataManager {
         // Create dataCollapsedQuality, the table where everything except read group and quality score has been collapsed
         qualityScoreCollapsedKey[0] = key[0]; // Make a new key with the read group ...
         qualityScoreCollapsedKey[1] = key[1]; //                                    and quality score
-        collapsedDatum = (RecalDatum) dataCollapsedQualityScore.get(qualityScoreCollapsedKey);
+        collapsedDatum = (RecalDatum) dataCollapsedQualityScore.get(errorModel).get(qualityScoreCollapsedKey);
         if (collapsedDatum == null) {
-            dataCollapsedQualityScore.put(new RecalDatum(fullDatum), qualityScoreCollapsedKey);
+            dataCollapsedQualityScore.get(errorModel).put(new RecalDatum(fullDatum), qualityScoreCollapsedKey);
         }
         else {
             collapsedDatum.increment(fullDatum);
         }
 
         // Create dataCollapsedByCovariate's, the tables where everything except read group, quality score, and given covariate has been collapsed
-        for (int iii = 0; iii < dataCollapsedByCovariate.size(); iii++) {
+        for (int iii = 0; iii < dataCollapsedByCovariate.get(errorModel).size(); iii++) {
             covariateCollapsedKey[0] = key[0]; // Make a new key with the read group ...
             covariateCollapsedKey[1] = key[1]; //                                    and quality score ...
             final Object theCovariateElement = key[iii + 2]; //                                        and the given covariate
             if (theCovariateElement != null) {
                 covariateCollapsedKey[2] = theCovariateElement;
-                collapsedDatum = (RecalDatum) dataCollapsedByCovariate.get(iii).get(covariateCollapsedKey);
+                collapsedDatum = (RecalDatum) dataCollapsedByCovariate.get(errorModel).get(iii).get(covariateCollapsedKey);
                 if (collapsedDatum == null) {
-                    dataCollapsedByCovariate.get(iii).put(new RecalDatum(fullDatum), covariateCollapsedKey);
+                    dataCollapsedByCovariate.get(errorModel).get(iii).put(new RecalDatum(fullDatum), covariateCollapsedKey);
                 }
                 else {
                     collapsedDatum.increment(fullDatum);
@@ -198,11 +207,13 @@ public class RecalDataManager {
      */
     public final void generateEmpiricalQualities(final int smoothing, final int maxQual) {
 
-        recursivelyGenerateEmpiricalQualities(dataCollapsedReadGroup.data, smoothing, maxQual);
+        for( final BaseRecalibrationType errorModel : BaseRecalibrationType.values() ) {
-        recursivelyGenerateEmpiricalQualities(dataCollapsedQualityScore.data, smoothing, maxQual);
+            recursivelyGenerateEmpiricalQualities(dataCollapsedReadGroup.get(errorModel).data, smoothing, maxQual);
-        for (NestedHashMap map : dataCollapsedByCovariate) {
+            recursivelyGenerateEmpiricalQualities(dataCollapsedQualityScore.get(errorModel).data, smoothing, maxQual);
-            recursivelyGenerateEmpiricalQualities(map.data, smoothing, maxQual);
+            for (NestedHashMap map : dataCollapsedByCovariate.get(errorModel)) {
-            checkForSingletons(map.data);
+                recursivelyGenerateEmpiricalQualities(map.data, smoothing, maxQual);
+                checkForSingletons(map.data);
+            }
         }
     }
 
@@ -241,15 +252,15 @@ public class RecalDataManager {
      * @param covariate Which covariate indexes the desired collapsed HashMap
      * @return The desired collapsed HashMap
      */
-    public final NestedHashMap getCollapsedTable(final int covariate) {
+    public final NestedHashMap getCollapsedTable(final int covariate, final BaseRecalibrationType errorModel) {
         if (covariate == 0) {
-            return dataCollapsedReadGroup; // Table where everything except read group has been collapsed
+            return dataCollapsedReadGroup.get(errorModel); // Table where everything except read group has been collapsed
         }
         else if (covariate == 1) {
-            return dataCollapsedQualityScore; // Table where everything except read group and quality score has been collapsed
+            return dataCollapsedQualityScore.get(errorModel); // Table where everything except read group and quality score has been collapsed
         }
         else {
-            return dataCollapsedByCovariate.get(covariate - 2); // Table where everything except read group, quality score, and given covariate has been collapsed
+            return dataCollapsedByCovariate.get(errorModel).get(covariate - 2); // Table where everything except read group, quality score, and given covariate has been collapsed
         }
     }
 
@@ -260,7 +271,7 @@ public class RecalDataManager {
      * @param RAC  The list of shared command line arguments
      */
     public static void parseSAMRecord(final GATKSAMRecord read, final RecalibrationArgumentCollection RAC) {
-        GATKSAMReadGroupRecord readGroup = ((GATKSAMRecord) read).getReadGroup();
+        GATKSAMReadGroupRecord readGroup = read.getReadGroup();
 
         if (RAC.FORCE_PLATFORM != null && (readGroup.getPlatform() == null || !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM))) {
             readGroup.setPlatform(RAC.FORCE_PLATFORM);

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ContextCovariate.java

@@ -56,7 +56,7 @@ public class ContextCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(final GATKSAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
         byte[] bases = read.getReadBases();
         for (int i = 0; i < read.getReadLength(); i++)
             comparable[i] = (i < CONTEXT_SIZE) ? allN : new String(Arrays.copyOfRange(bases, i - CONTEXT_SIZE, i));

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java

@@ -378,7 +378,7 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
                     }
 
                     RecalDataManager.parseColorSpace(gatkRead);
-                    gatkRead.setTemporaryAttribute(COVARS_ATTRIBUTE, RecalDataManager.computeCovariates(gatkRead, requestedCovariates, BaseRecalibration.BaseRecalibrationType.BASE_SUBSTITUTION));
+                    gatkRead.setTemporaryAttribute(COVARS_ATTRIBUTE, RecalDataManager.computeCovariates(gatkRead, requestedCovariates));
                 }
 
                 // Skip this position if base quality is zero

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java

@@ -43,7 +43,7 @@ public interface Covariate {
 
     public Comparable getValue(String str); // Used to get the covariate's value from input csv file in TableRecalibrationWalker
 
-    public void getValues(GATKSAMRecord read, Comparable[] comparable, BaseRecalibration.BaseRecalibrationType modelType);
+    public void getValues(GATKSAMRecord 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/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java

@@ -66,7 +66,7 @@ public class CycleCovariate implements StandardCovariate {
 
     // Used to pick out the covariate's value from attributes of the read
     @Override
-    public void getValues(final GATKSAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
 
         //-----------------------------
         // Illumina, Solid, PacBio, and Complete Genomics

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java

@@ -66,7 +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(final GATKSAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
         final HashMap<Integer, Dinuc> dinucHashMapRef = this.dinucHashMap; //optimize access to dinucHashMap
         final int readLength = read.getReadLength();
         final boolean negativeStrand = read.getReadNegativeStrandFlag();

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/GCContentCovariate.java

@@ -82,7 +82,7 @@ public class GCContentCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(final GATKSAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
         for (int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java

@@ -95,7 +95,7 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(final GATKSAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
         for (int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java

@@ -55,7 +55,7 @@ public class MappingQualityCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(final GATKSAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
         for (int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read); // BUGBUG: this can be optimized
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java

@@ -65,7 +65,7 @@ public class MinimumNQSCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(final GATKSAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
         for (int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java

@@ -55,7 +55,7 @@ public class PositionCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(final GATKSAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
         for (int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java

@@ -62,7 +62,7 @@ public class PrimerRoundCovariate implements ExperimentalCovariate {
     }
 
     @Override
-    public void getValues(final GATKSAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
         for (int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java

@@ -46,16 +46,10 @@ public class QualityScoreCovariate implements RequiredCovariate {
     }
 
     @Override
-    public void getValues(final GATKSAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
-        if (modelType == BaseRecalibration.BaseRecalibrationType.BASE_SUBSTITUTION) {
+        byte[] baseQualities = read.getBaseQualities();
-            byte[] baseQualities = read.getBaseQualities();
+        for (int i = 0; i < read.getReadLength(); i++) {
-            for (int i = 0; i < read.getReadLength(); i++) {
+            comparable[i] = (int) baseQualities[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
         }
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java

@@ -44,7 +44,7 @@ public class ReadGroupCovariate implements RequiredCovariate {
     }
 
     @Override
-    public void getValues(final GATKSAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
         final String readGroupId = read.getReadGroup().getReadGroupId();
         for (int i = 0; i < read.getReadLength(); i++) {
             comparable[i] = readGroupId;

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java

@@ -63,7 +63,6 @@ public class RecalDataManager {
     public final static String COLOR_SPACE_QUAL_ATTRIBUTE_TAG = "CQ"; // The tag that holds the color space quality scores for SOLID bams
     public final static String COLOR_SPACE_ATTRIBUTE_TAG = "CS"; // The tag that holds the color space for SOLID bams
     public final static String COLOR_SPACE_INCONSISTENCY_TAG = "ZC"; // A new tag made up for the recalibrator which will hold an array of ints which say if this base is inconsistent with its color
-    private static boolean warnUserNullReadGroup = false;
     private static boolean warnUserNullPlatform = false;
 
     public enum SOLID_RECAL_MODE {
@@ -604,7 +603,7 @@ 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, final BaseRecalibration.BaseRecalibrationType modelType) {
+    public static Comparable[][] computeCovariates(final GATKSAMRecord gatkRead, final List<Covariate> requestedCovariates) {
         //compute all covariates for this read
         final int numRequestedCovariates = requestedCovariates.size();
         final int readLength = gatkRead.getReadLength();
@@ -613,7 +612,7 @@ public class RecalDataManager {
         final Comparable[] tempCovariateValuesHolder = new Comparable[readLength];
 
         for (int i = 0; i < numRequestedCovariates; i++) {                              // Loop through the list of requested covariates and compute the values of each covariate for all positions in this read
-            requestedCovariates.get(i).getValues(gatkRead, tempCovariateValuesHolder, modelType);
+            requestedCovariates.get(i).getValues(gatkRead, tempCovariateValuesHolder);
             for (int j = 0; j < readLength; j++)
                 covariateValues_offset_x_covar[j][i] = tempCovariateValuesHolder[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.
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java

@@ -405,7 +405,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         }
 
         //compute all covariate values for this read
-        final Comparable[][] covariateValues_offset_x_covar = RecalDataManager.computeCovariates(read, requestedCovariates, BaseRecalibration.BaseRecalibrationType.BASE_SUBSTITUTION);
+        final Comparable[][] covariateValues_offset_x_covar = RecalDataManager.computeCovariates(read, requestedCovariates);
 
         // For each base in the read
         for (int offset = 0; offset < read.getReadLength(); offset++) {

public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java

@@ -25,14 +25,12 @@
 
 package org.broadinstitute.sting.utils.recalibration;
 
-import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate;
+import org.broadinstitute.sting.gatk.walkers.bqsr.*;
-import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDataManager;
-import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
-import org.broadinstitute.sting.gatk.walkers.recalibration.RecalibrationArgumentCollection;
 import org.broadinstitute.sting.utils.QualityUtils;
 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.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.text.XReadLines;
@@ -52,19 +50,13 @@ import java.util.regex.Pattern;
 
 public class BaseRecalibration {
 
-    public enum BaseRecalibrationType {
-        BASE_SUBSTITUTION,
-        BASE_INSERTION,
-        BASE_DELETION
-    }
-
     private RecalDataManager dataManager; // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
     private final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // List of covariates to be used in this calculation
     public static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
     public static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
     public static final String EOF_MARKER = "EOF";
     private static final int MAX_QUALITY_SCORE = 65; //BUGBUG: what value to use here?
-    private NestedHashMap qualityScoreByFullCovariateKey = new NestedHashMap(); // Caches the result of performSequentialQualityCalculation(..) for all sets of covariate values.
+    private NestedHashMap qualityScoreByFullCovariateKey = new NestedHashMap(); // Caches the result of performSequentialQualityCalculation(...) for all sets of covariate values.
 
     public BaseRecalibration( final File RECAL_FILE ) {
         // Get a list of all available covariates
@@ -89,7 +81,7 @@ public class BaseRecalibration {
                         throw new UserException.MalformedFile( RECAL_FILE, "Malformed input recalibration file. Found covariate names intermingled with data in file: " + RECAL_FILE );
                     } else { // Found the covariate list in input file, loop through all of them and instantiate them
                         String[] vals = line.split(",");
-                        for( int iii = 0; iii < vals.length - 3; iii++ ) { // There are n-3 covariates. The last three items are nObservations, nMismatch, and Qempirical
+                        for( int iii = 0; iii < vals.length - 4; iii++ ) { // There are n-4 covariates. The last four items are ErrorModel, nObservations, nMismatch, and Qempirical
                             boolean foundClass = false;
                             for( Class<?> covClass : classes ) {
                                 if( (vals[iii] + "Covariate").equalsIgnoreCase( covClass.getSimpleName() ) ) {
@@ -160,7 +152,7 @@ public class BaseRecalibration {
         final String[] vals = line.split(",");
 
         // Check if the data line is malformed, for example if the read group string contains a comma then it won't be parsed correctly
-        if( vals.length != requestedCovariates.size() + 3 ) { // +3 because of nObservations, nMismatch, and Qempirical
+        if( vals.length != requestedCovariates.size() + 4 ) { // +4 because of ErrorModel, nObservations, nMismatch, and Qempirical
             throw new UserException.MalformedFile(file, "Malformed input recalibration file. Found data line with too many fields: " + line +
                     " --Perhaps the read group string contains a comma and isn't being parsed correctly.");
         }
@@ -172,39 +164,63 @@ public class BaseRecalibration {
             cov = requestedCovariates.get( iii );
             key[iii] = cov.getValue( vals[iii] );
         }
-
+        final String modelString = vals[iii++];
+        final RecalDataManager.BaseRecalibrationType errorModel = ( modelString.equals(CovariateKeySet.mismatchesCovariateName) ? RecalDataManager.BaseRecalibrationType.BASE_SUBSTITUTION :
+            ( modelString.equals(CovariateKeySet.insertionsCovariateName) ? RecalDataManager.BaseRecalibrationType.BASE_INSERTION :
+            ( modelString.equals(CovariateKeySet.deletionsCovariateName) ? RecalDataManager.BaseRecalibrationType.BASE_DELETION : null ) ) );
+                
         // Create a new datum using the number of observations, number of mismatches, and reported quality score
         final RecalDatum datum = new RecalDatum( Long.parseLong( vals[iii] ), Long.parseLong( vals[iii + 1] ), Double.parseDouble( vals[1] ), 0.0 );
         // Add that datum to all the collapsed tables which will be used in the sequential calculation
-        dataManager.addToAllTables( key, datum, QualityUtils.MIN_USABLE_Q_SCORE ); //BUGBUG: used to be Q5 now is Q6, probably doesn't matter
+        
+        dataManager.addToAllTables( key, datum, QualityUtils.MIN_USABLE_Q_SCORE, errorModel ); //BUGBUG: used to be Q5 now is Q6, probably doesn't matter
     }
     
-    public byte[] recalibrateRead( final GATKSAMRecord read, final byte[] originalQuals, final BaseRecalibrationType modelType ) {
+    public void recalibrateRead( final GATKSAMRecord read ) {
 
-        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);
+        final CovariateKeySet covariateKeySet = RecalDataManager.getAllCovariateValuesFor( read );
-    
+
-        // For each base in the read
+        for( final RecalDataManager.BaseRecalibrationType errorModel : RecalDataManager.BaseRecalibrationType.values() ) {
-        for( int offset = 0; offset < read.getReadLength(); offset++ ) {
+            final byte[] originalQuals = ( errorModel == RecalDataManager.BaseRecalibrationType.BASE_SUBSTITUTION ? read.getBaseQualities() :
-    
+                ( errorModel == RecalDataManager.BaseRecalibrationType.BASE_INSERTION ? read.getBaseDeletionQualities() :
-            final Object[] fullCovariateKey = covariateValues_offset_x_covar[offset];
+                ( errorModel == RecalDataManager.BaseRecalibrationType.BASE_DELETION ? read.getBaseDeletionQualities() : null ) ) );
-    
+            final byte[] recalQuals = originalQuals.clone();
-            Byte qualityScore = (Byte) qualityScoreByFullCovariateKey.get(fullCovariateKey);
+
-            if(qualityScore == null)
+            // For each base in the read
-            {
+            for( int offset = 0; offset < read.getReadLength(); offset++ ) {
-                qualityScore = performSequentialQualityCalculation( fullCovariateKey );
-                qualityScoreByFullCovariateKey.put(qualityScore, fullCovariateKey);
-            }
-    
-            recalQuals[offset] = qualityScore;
-        }
-    
-        preserveQScores( originalQuals, recalQuals ); // Overwrite the work done if original quality score is too low
         
-        return recalQuals;
+                final Object[] fullCovariateKey =
+                        ( errorModel == RecalDataManager.BaseRecalibrationType.BASE_SUBSTITUTION ? covariateKeySet.getMismatchesKeySet(offset) :
+                        ( errorModel == RecalDataManager.BaseRecalibrationType.BASE_INSERTION ? covariateKeySet.getInsertionsKeySet(offset) :
+                        ( errorModel == RecalDataManager.BaseRecalibrationType.BASE_DELETION ? covariateKeySet.getDeletionsKeySet(offset) : null ) ) );
+        
+                Byte qualityScore = (Byte) qualityScoreByFullCovariateKey.get(fullCovariateKey);
+                if( qualityScore == null ) {
+                    qualityScore = performSequentialQualityCalculation( errorModel, fullCovariateKey );
+                    qualityScoreByFullCovariateKey.put(qualityScore, fullCovariateKey);
+                }
+        
+                recalQuals[offset] = qualityScore;
+            }
+        
+            preserveQScores( originalQuals, recalQuals ); // Overwrite the work done if original quality score is too low
+            switch (errorModel) {
+                case BASE_SUBSTITUTION:
+                    read.setBaseQualities( recalQuals );
+                    break;
+                case BASE_INSERTION:
+                    read.setAttribute( GATKSAMRecord.BQSR_BASE_INSERTION_QUALITIES, recalQuals );
+                    break;
+                case BASE_DELETION:
+                    read.setAttribute( GATKSAMRecord.BQSR_BASE_DELETION_QUALITIES, recalQuals );
+                    break;
+                default:
+                    throw new ReviewedStingException("Unrecognized Base Recalibration type: " + errorModel );
+            }
+        }
+       
     }
 
     /**
@@ -222,7 +238,7 @@ public class BaseRecalibration {
      * @param key The list of Comparables that were calculated from the covariates
      * @return A recalibrated quality score as a byte
      */
-    private byte performSequentialQualityCalculation( final Object... key ) {
+    private byte performSequentialQualityCalculation( final RecalDataManager.BaseRecalibrationType errorModel, final Object... key ) {
 
         final byte qualFromRead = (byte)Integer.parseInt(key[1].toString());
         final Object[] readGroupCollapsedKey = new Object[1];
@@ -231,7 +247,7 @@ public class BaseRecalibration {
 
         // The global quality shift (over the read group only)
         readGroupCollapsedKey[0] = key[0];
-        final RecalDatum globalRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(0).get( readGroupCollapsedKey ));
+        final RecalDatum globalRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(0, errorModel).get( readGroupCollapsedKey ));
         double globalDeltaQ = 0.0;
         if( globalRecalDatum != null ) {
             final double globalDeltaQEmpirical = globalRecalDatum.getEmpiricalQuality();
@@ -242,7 +258,7 @@ public class BaseRecalibration {
         // The shift in quality between reported and empirical
         qualityScoreCollapsedKey[0] = key[0];
         qualityScoreCollapsedKey[1] = key[1];
-        final RecalDatum qReportedRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(1).get( qualityScoreCollapsedKey ));
+        final RecalDatum qReportedRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(1, errorModel).get( qualityScoreCollapsedKey ));
         double deltaQReported = 0.0;
         if( qReportedRecalDatum != null ) {
             final double deltaQReportedEmpirical = qReportedRecalDatum.getEmpiricalQuality();
@@ -256,7 +272,7 @@ public class BaseRecalibration {
         covariateCollapsedKey[1] = key[1];
         for( int iii = 2; iii < key.length; iii++ ) {
             covariateCollapsedKey[2] =  key[iii]; // The given covariate
-            final RecalDatum covariateRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(iii).get( covariateCollapsedKey ));
+            final RecalDatum covariateRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(iii, errorModel).get( covariateCollapsedKey ));
             if( covariateRecalDatum != null ) {
                 deltaQCovariateEmpirical = covariateRecalDatum.getEmpiricalQuality();
                 deltaQCovariates += ( deltaQCovariateEmpirical - qualFromRead - (globalDeltaQ + deltaQReported) );
@@ -265,18 +281,6 @@ public class BaseRecalibration {
 
         final double newQuality = qualFromRead + globalDeltaQ + deltaQReported + deltaQCovariates;
         return QualityUtils.boundQual( (int)Math.round(newQuality), (byte)MAX_QUALITY_SCORE );
-
-        // Verbose printouts used to validate with old recalibrator
-        //if(key.contains(null)) {
-        //    System.out.println( key  + String.format(" => %d + %.2f + %.2f + %.2f + %.2f = %d",
-        //                 qualFromRead, globalDeltaQ, deltaQReported, deltaQPos, deltaQDinuc, newQualityByte));
-        //}
-        //else {
-        //    System.out.println( String.format("%s %s %s %s => %d + %.2f + %.2f + %.2f + %.2f = %d",
-        //                 key.get(0).toString(), key.get(3).toString(), key.get(2).toString(), key.get(1).toString(), qualFromRead, globalDeltaQ, deltaQReported, deltaQPos, deltaQDinuc, newQualityByte) );
-        //}
-
-        //return newQualityByte;
     }
 
     /**
@@ -291,5 +295,4 @@ public class BaseRecalibration {
             }
         }
     }
-
 }

public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java

@@ -54,7 +54,6 @@ public class GATKSAMRecord extends BAMRecord {
     // Base Quality Score Recalibrator specific attribute tags
     public static final String BQSR_BASE_INSERTION_QUALITIES = "BI";
     public static final String BQSR_BASE_DELETION_QUALITIES = "BD";
-    public static final String BQSR_BASES_HAVE_BEEN_RECALIBRATED_TAG = "BR";
 
     // the SAMRecord data we're caching
     private String mReadString = null;
@@ -163,27 +162,6 @@ public class GATKSAMRecord extends BAMRecord {
         return super.equals(o);
     }
 
-
-    @Override
-    public byte[] getBaseQualities() {
-        return super.getBaseQualities();
-        /*
-        if( getAttribute( BQSR_BASES_HAVE_BEEN_RECALIBRATED_TAG ) != null ) {
-            return super.getBaseQualities();
-        } else {
-            // if the recal data was populated in the engine then recalibrate the quality scores on the fly
-            if( GenomeAnalysisEngine.hasBaseRecalibration() ) {
-                final byte[] quals = GenomeAnalysisEngine.getBaseRecalibration().recalibrateRead( this, super.getBaseQualities() );
-                setBaseQualities(quals);
-                setAttribute( BQSR_BASES_HAVE_BEEN_RECALIBRATED_TAG, true );
-                return quals;
-            } else { // just use the qualities that are in the read since we don't have the sufficient information to recalibrate on the fly
-                return super.getBaseQualities();
-            }
-        }
-        */
-    }
-
     /**
      * Accessors for base insertion and base deletion quality scores
      */
@@ -191,13 +169,8 @@ public class GATKSAMRecord extends BAMRecord {
         byte[] quals = getByteArrayAttribute( BQSR_BASE_INSERTION_QUALITIES );
         if( quals == null ) {
             quals = new byte[getBaseQualities().length];
-            Arrays.fill(quals, (byte) 45); // allow for differing default values between BaseInsertions and BaseDeletions
+            Arrays.fill(quals, (byte) 45); // Some day in the future when base insertion and base deletion quals exist the samtools API will
-            // if the recal data was populated in the engine then recalibrate the quality scores on the fly
+            // be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45
-            // else give default values which are flat Q45
-            if( GenomeAnalysisEngine.hasBaseRecalibration() ) {
-                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 );
         }
         return quals;
@@ -207,13 +180,8 @@ public class GATKSAMRecord extends BAMRecord {
         byte[] quals = getByteArrayAttribute( BQSR_BASE_DELETION_QUALITIES );
         if( quals == null ) {
             quals = new byte[getBaseQualities().length];
-            Arrays.fill(quals, (byte) 45);
+            Arrays.fill(quals, (byte) 45); // Some day in the future when base insertion and base deletion quals exist the samtools API will
-            // if the recal data was populated in the engine then recalibrate the quality scores on the fly
+            // be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45
-            // else give default values which are flat Q45
-            if( GenomeAnalysisEngine.hasBaseRecalibration() ) {
-                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 );
         }
         return quals;