Cleaning up the covariate classes and removing unused code from the bqsr optimizations in 2009.

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -215,8 +215,8 @@ public class GenomeAnalysisEngine {
             resetRandomGenerator(System.currentTimeMillis());
 
         // if the use specified an input BQSR recalibration table then enable on the fly recalibration
-        if (this.getArguments().RECAL_FILE != null)
+        if (this.getArguments().BQSR_RECAL_FILE != null)
-            setBaseRecalibration(this.getArguments().RECAL_FILE);
+            setBaseRecalibration(this.getArguments().BQSR_RECAL_FILE);
 
         // Determine how the threads should be divided between CPU vs. IO.
         determineThreadAllocation();

public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -192,7 +192,7 @@ public class GATKArgumentCollection {
      * and the raw empirical quality score calculated by phred-scaling the mismatch rate.
      */
     @Input(fullName="BQSR", shortName="BQSR", required=false, doc="Filename for the input covariates table recalibration .csv file which enables on the fly base quality score recalibration")
-    public File RECAL_FILE = null; // BUGBUG: need a better argument name once we decide how BQSRs v1 and v2 will live in the code base simultaneously
+    public File BQSR_RECAL_FILE = null; // BUGBUG: need a better argument name once we decide how BQSRs v1 and v2 will live in the code base simultaneously
 
     @Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false)
     public byte defaultBaseQualities = -1;

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

@@ -41,12 +41,14 @@ public class ContextCovariate implements Covariate {
     String allN = "";
 
     // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
     public void initialize( final RecalibrationArgumentCollection RAC ) {
         for( int iii = 0; iii < CONTEXT_SIZE; iii++ ) {
             allN += "N";
         }
     }
 
+    @Override
     public void getValues(SAMRecord read, Comparable[] comparable) {
         byte[] bases = read.getReadBases();
         for(int i = 0; i < read.getReadLength(); i++) {
@@ -55,8 +57,8 @@ public class ContextCovariate implements Covariate {
     }
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
     public final Comparable getValue( final String str ) {
         return str;
     }
-
 }

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

@@ -51,6 +51,7 @@ public class CycleCovariate implements StandardCovariate {
     private final static EnumSet<NGSPlatform> FLOW_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.LS454,  NGSPlatform.ION_TORRENT);
 
     // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
     public void initialize( final RecalibrationArgumentCollection RAC ) {
         if( RAC.DEFAULT_PLATFORM != null ) {
             if( RAC.DEFAULT_PLATFORM.equalsIgnoreCase( "SLX" ) || RAC.DEFAULT_PLATFORM.equalsIgnoreCase( "ILLUMINA" ) ||
@@ -63,6 +64,7 @@ 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) {
 
         //-----------------------------
@@ -164,6 +166,7 @@ public class CycleCovariate implements StandardCovariate {
     }
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
     public final Comparable getValue( final String str ) {
         return Integer.parseInt( str );
     }

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

@@ -48,6 +48,7 @@ public class DinucCovariate implements StandardCovariate {
     private HashMap<Integer, Dinuc> dinucHashMap;
 
     // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
     public void initialize( final RecalibrationArgumentCollection RAC ) {
         final byte[] BASES = { (byte)'A', (byte)'C', (byte)'G', (byte)'T' };
         dinucHashMap = new HashMap<Integer, Dinuc>();
@@ -60,44 +61,10 @@ public class DinucCovariate implements StandardCovariate {
         dinucHashMap.put( Dinuc.hashBytes(NO_CALL, NO_CALL), NO_DINUC );
     }
 
-    /*
-    // Used to pick out the covariate's value from attributes of the read
-    public final Comparable getValue( final SAMRecord read, final int offset ) {
-
-        byte base;
-        byte prevBase;
-        final byte[] bases = read.getReadBases();
-        // If this is a negative strand read then we need to reverse the direction for our previous base
-        if( read.getReadNegativeStrandFlag() ) {
-            // No dinuc at the beginning of the read
-            if( offset == bases.length-1 ) {
-                return NO_DINUC;
-            }
-            base = (byte)BaseUtils.simpleComplement( (char)(bases[offset]) );
-            // Note: We are using the previous base in the read, not the previous base in the reference. This is done in part to be consistent with unmapped reads.
-            prevBase = (byte)BaseUtils.simpleComplement( (char)(bases[offset + 1]) );
-        } else {
-            // No dinuc at the beginning of the read
-            if( offset == 0 ) {
-                return NO_DINUC;
-            }
-            base = bases[offset];
-            // Note: We are using the previous base in the read, not the previous base in the reference. This is done in part to be consistent with unmapped reads.
-            prevBase = bases[offset - 1];
-        }
-
-        // Make sure the previous base is good
-        if( !BaseUtils.isRegularBase( prevBase ) ) {
-            return NO_DINUC;
-        }
-
-        return dinucHashMap.get( Dinuc.hashBytes( prevBase, base ) );
-    }
-    */
-
     /**
      * 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 ) {
         final HashMap<Integer, Dinuc> dinucHashMapRef = this.dinucHashMap; //optimize access to dinucHashMap
         final int readLength = read.getReadLength();
@@ -134,6 +101,7 @@ public class DinucCovariate implements StandardCovariate {
     }
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
     public final Comparable getValue( final String str ) {
         byte[] bytes = str.getBytes();
         final Dinuc returnDinuc = dinucHashMap.get( Dinuc.hashBytes( bytes[0], bytes[1] ) );
@@ -143,7 +111,6 @@ public class DinucCovariate implements StandardCovariate {
         return returnDinuc;
     }
 
-
     /**
      * Reverses the given array in place.
      *

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

@@ -41,12 +41,13 @@ public class GCContentCovariate implements ExperimentalCovariate {
     int numBack = 7;
 
     // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
     public void initialize( final RecalibrationArgumentCollection RAC ) {
         numBack = RAC.HOMOPOLYMER_NBACK;
     }
 
     // Used to pick out the covariate's value from attributes of the read
-    public final Comparable getValue( final SAMRecord read, final int offset ) {
+    private final Comparable getValue( final SAMRecord read, final int offset ) {
 
         // ATTGCCCCGTAAAAAAAGAGAA
         // 0000123456654321001122
@@ -75,7 +76,8 @@ public class GCContentCovariate implements ExperimentalCovariate {
             return -1;
         }
     }
-    
+
+    @Override
     public void getValues(SAMRecord read, Comparable[] comparable) {
         for(int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
@@ -83,10 +85,8 @@ public class GCContentCovariate implements ExperimentalCovariate {
     }
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
     public final Comparable getValue( final String str ) {
         return Integer.parseInt( str );
     }
-
-
-
 }

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

@@ -43,12 +43,13 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
     int numBack = 7;
 
     // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
     public void initialize( final RecalibrationArgumentCollection RAC ) {
         numBack = RAC.HOMOPOLYMER_NBACK;
     }
 
     // Used to pick out the covariate's value from attributes of the read
-    public final Comparable getValue( final SAMRecord read, final int offset ) {
+    private final Comparable getValue( final SAMRecord read, final int offset ) {
 
         // This block of code is for if you don't want to only count consecutive bases
         // ATTGCCCCGTAAAAAAAAATA
@@ -90,6 +91,7 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
         return numAgree;
     }
 
+    @Override
     public void getValues(SAMRecord read, Comparable[] comparable) {
         for(int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
@@ -97,8 +99,8 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
     }
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
     public final Comparable getValue( final String str ) {
         return Integer.parseInt( str );
     }
-
 }

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

@@ -38,23 +38,25 @@ import net.sf.samtools.SAMRecord;
 public class MappingQualityCovariate implements ExperimentalCovariate {
 
     // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
     public void initialize( final RecalibrationArgumentCollection RAC ) {
     }
 
     // Used to pick out the covariate's value from attributes of the read
-    public final Comparable getValue( final SAMRecord read, final int offset ) {
+    private final Comparable getValue( final SAMRecord read, final int offset ) {
         return read.getMappingQuality();
     }
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
     public final Comparable getValue( final String str ) {
         return Integer.parseInt( str );
     }
 
+    @Override
     public void getValues(SAMRecord read, 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/MinimumNQSCovariate.java

@@ -41,12 +41,13 @@ public class MinimumNQSCovariate implements ExperimentalCovariate {
     private int windowReach; // How far in each direction from the current base to look
 
     // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
     public void initialize( final RecalibrationArgumentCollection RAC ) {
         windowReach = RAC.WINDOW_SIZE / 2; // integer division
     }
 
     // Used to pick out the covariate's value from attributes of the read
-    public final Comparable getValue( final SAMRecord read, final int offset ) {
+    private final Comparable getValue( final SAMRecord read, final int offset ) {
 
         // Loop over the list of base quality scores in the window and find the minimum
         final byte[] quals = read.getBaseQualities();
@@ -61,14 +62,16 @@ public class MinimumNQSCovariate implements ExperimentalCovariate {
         return minQual;
     }
 
-    // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
-    public final Comparable getValue( final String str ) {
-        return Integer.parseInt( str );
-    }
-
     public void getValues(SAMRecord read, Comparable[] comparable) {
         for(int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }
     }
+
+    // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
+    public final Comparable getValue( final String str ) {
+        return Integer.parseInt( str );
+    }
 }

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

@@ -39,11 +39,12 @@ import net.sf.samtools.SAMRecord;
 public class PositionCovariate implements ExperimentalCovariate {
 
     // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
     public void initialize( final RecalibrationArgumentCollection RAC ) {
     }
 
     // Used to pick out the covariate's value from attributes of the read
-    public final Comparable getValue( final SAMRecord read, final int offset ) {
+    private final Comparable getValue( final SAMRecord read, final int offset ) {
         int cycle = offset;
         if( read.getReadNegativeStrandFlag() ) {
             cycle = read.getReadLength() - (offset + 1);
@@ -51,15 +52,16 @@ public class PositionCovariate implements ExperimentalCovariate {
         return cycle;
     }
 
-    // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
-    public final Comparable getValue( final String str ) {
-        return Integer.parseInt( str );
-    }
-
     public void getValues(SAMRecord read, Comparable[] comparable) {
         for(int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }
     }
 
+    // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
+    public final Comparable getValue( final String str ) {
+        return Integer.parseInt( str );
+    }
 }

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

@@ -40,11 +40,12 @@ import net.sf.samtools.SAMRecord;
 public class PrimerRoundCovariate implements ExperimentalCovariate {
 
     // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
     public void initialize( final RecalibrationArgumentCollection RAC ) {
     }
 
     // Used to pick out the covariate's value from attributes of the read
-    public final Comparable getValue( final SAMRecord read, final int offset ) {
+    private final Comparable getValue( final SAMRecord read, final int offset ) {
         if( read.getReadGroup().getPlatform().equalsIgnoreCase( "SOLID" ) || read.getReadGroup().getPlatform().equalsIgnoreCase( "ABI_SOLID" ) ) {
             int pos = offset;
             if( read.getReadNegativeStrandFlag() ) {
@@ -57,14 +58,16 @@ public class PrimerRoundCovariate implements ExperimentalCovariate {
 
     }
 
-    // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
-    public final Comparable getValue( final String str ) {
-        return Integer.parseInt( str );
-    }
-
     public void getValues(SAMRecord read, Comparable[] comparable) {
         for(int iii = 0; iii < read.getReadLength(); iii++) {
             comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
         }
     }
+
+    // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
+    public final Comparable getValue( final String str ) {
+        return Integer.parseInt( str );
+    }
 }

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

@@ -38,16 +38,11 @@ import net.sf.samtools.SAMRecord;
 public class QualityScoreCovariate implements RequiredCovariate {
 
     // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
     public void initialize( final RecalibrationArgumentCollection RAC ) {
     }
 
-    /*
+    @Override
-    // Used to pick out the covariate's value from attributes of the read
-    public final Comparable getValue( final SAMRecord read, final int offset ) {
-        return (int)(read.getBaseQualities()[offset]);
-    }
-    */
-
     public void getValues(SAMRecord read, Comparable[] comparable) {
         byte[] baseQualities = read.getBaseQualities();
         for(int i = 0; i < read.getReadLength(); i++) {
@@ -56,8 +51,8 @@ public class QualityScoreCovariate implements RequiredCovariate {
     }
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
     public final Comparable getValue( final String str ) {
         return Integer.parseInt( str );
     }
-
 }

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

@@ -40,16 +40,11 @@ public class ReadGroupCovariate implements RequiredCovariate{
     public static final String defaultReadGroup = "DefaultReadGroup";
 
     // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
     public void initialize( final RecalibrationArgumentCollection RAC ) {
     }
 
-    /*
+    @Override
-    // Used to pick out the covariate's value from attributes of the read
-    public final Comparable getValue( final SAMRecord read, final int offset ) {
-        return read.getReadGroup().getReadGroupId();
-    }
-    */
-
     public void getValues(SAMRecord read, Comparable[] comparable) {
         final String readGroupId = read.getReadGroup().getReadGroupId();
         for(int i = 0; i < read.getReadLength(); i++) {
@@ -58,10 +53,10 @@ public class ReadGroupCovariate implements RequiredCovariate{
     }
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
+    @Override
     public final Comparable getValue( final String str ) {
         return str;
     }
-
 }
 
 

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

@@ -162,9 +162,11 @@ 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 {
@@ -178,8 +180,8 @@ public class GATKSAMRecord extends BAMRecord {
                 return super.getBaseQualities();
             }
         }
+        */
     }
-    */
 
     /**
      * Accessors for base insertion and base deletion quality scores