A quick implementation of the experimental covariates for the TGen folks to work with.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3344 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -39,7 +39,6 @@ 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( SAMRecord read, int offset ); // Used to pick out the covariate's value from attributes of the read
     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

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

@@ -61,6 +61,7 @@ public class CycleCovariate implements StandardCovariate {
         }
     }
 
+    /*
     // Used to pick out the covariate's value from attributes of the read
     public final Comparable getValue( final SAMRecord read, final int offset ) {
 
@@ -158,8 +159,9 @@ public class CycleCovariate implements StandardCovariate {
 
         return cycle;
     }
+    */
 
-
+    // Used to pick out the covariate's value from attributes of the read
     public void getValues(SAMRecord read, Comparable[] comparable) {
 
         //-----------------------------

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

@@ -61,6 +61,7 @@ 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 ) {
 
@@ -93,7 +94,7 @@ public class DinucCovariate implements StandardCovariate {
 
         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.

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

@@ -77,7 +77,9 @@ public class GCContentCovariate implements ExperimentalCovariate {
     }
     
     public void getValues(SAMRecord read, Comparable[] comparable) {
-        throw new IllegalStateException("Not yet implemented");
+        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

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

@@ -91,7 +91,9 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
     }
 
     public void getValues(SAMRecord read, Comparable[] comparable) {
-        throw new IllegalStateException("Not yet implemented");
+        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

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

@@ -52,7 +52,9 @@ public class MappingQualityCovariate implements ExperimentalCovariate {
     }
 
     public void getValues(SAMRecord read, Comparable[] comparable) {
-        throw new IllegalStateException("Not yet implemented");
+        for(int iii = 0; iii < read.getReadLength(); iii++) {
+            comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
+        }
     }
 
 }

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

@@ -67,6 +67,8 @@ public class MinimumNQSCovariate implements ExperimentalCovariate {
     }
 
     public void getValues(SAMRecord read, Comparable[] comparable) {
-        throw new IllegalStateException("Not yet implemented");
+        for(int iii = 0; iii < read.getReadLength(); iii++) {
+            comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
+        }
     }
 }

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

@@ -57,7 +57,9 @@ public class PositionCovariate implements ExperimentalCovariate {
     }
 
     public void getValues(SAMRecord read, Comparable[] comparable) {
-        throw new IllegalStateException("Not yet implemented");
+        for(int iii = 0; iii < read.getReadLength(); iii++) {
+            comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
+        }
     }
 
 }

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

@@ -45,7 +45,7 @@ public class PrimerRoundCovariate implements ExperimentalCovariate {
 
     // Used to pick out the covariate's value from attributes of the read
     public final Comparable getValue( final SAMRecord read, final int offset ) {
-        if( read.getReadGroup().getPlatform().equalsIgnoreCase( "SOLID" ) ) {
+        if( read.getReadGroup().getPlatform().equalsIgnoreCase( "SOLID" ) || read.getReadGroup().getPlatform().equalsIgnoreCase( "ABI_SOLID" ) ) {
             int pos = offset;
             if( read.getReadNegativeStrandFlag() ) {
                 pos = read.getReadLength() - (offset + 1);
@@ -63,6 +63,8 @@ public class PrimerRoundCovariate implements ExperimentalCovariate {
     }
 
     public void getValues(SAMRecord read, Comparable[] comparable) {
-        throw new IllegalStateException("Not yet implemented");
+        for(int iii = 0; iii < read.getReadLength(); iii++) {
+            comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
+        }
     }
 }

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

@@ -41,10 +41,12 @@ public class QualityScoreCovariate implements RequiredCovariate {
     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 ) {
         return (int)(read.getBaseQualities()[offset]);
     }
+    */
 
     public void getValues(SAMRecord read, Comparable[] comparable) {
         byte[] baseQualities = read.getBaseQualities();

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

@@ -43,10 +43,12 @@ public class ReadGroupCovariate implements RequiredCovariate{
     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 ) {
         return read.getReadGroup().getReadGroupId();
     }
+    */
 
     public void getValues(SAMRecord read, Comparable[] comparable) {
         final String readGroupId = read.getReadGroup().getReadGroupId();

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java

@@ -41,6 +41,7 @@ public class TileCovariate implements ExperimentalCovariate {
         exceptionWhenNoTile = RAC.EXCEPTION_IF_NO_TILE;
     }
 
+
     // Used to pick out the covariate's value from attributes of the read
     public Comparable getValue(final SAMRecord read, final int offset) {
         Integer tile = IlluminaUtil.getTileFromReadName(read.getReadName());