Removed silly casts from Integer to int.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2164 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -103,7 +103,7 @@ public class CycleCovariate implements Covariate {
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
     public final Comparable getValue( final String str ) {
-        return (int)Integer.parseInt( str ); // Cast to primitive int (as opposed to Integer Object) is required so that the return value from the two getValue methods hash to same thing
+        return Integer.parseInt( str );
     }
 
     // Used to estimate the amount space required for the full data HashMap

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

@@ -46,7 +46,7 @@ public class MappingQualityCovariate implements Covariate {
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
     public final Comparable getValue( final String str ) {
-        return (int)Integer.parseInt( str ); // cast to primitive int (as opposed to Integer Object) is required so that the return value from the two getValue methods hash to same thing
+        return Integer.parseInt( str );
     }
 
     // Used to estimate the amount space required for the full data HashMap

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

@@ -63,7 +63,7 @@ public class MinimumNQSCovariate implements Covariate {
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
     public final Comparable getValue( final String str ) {
-        return (int)Integer.parseInt( str ); // cast to primitive int (as opposed to Integer Object) is required so that the return value from the two getValue methods hash to same thing
+        return Integer.parseInt( str );
     }
 
     // Used to estimate the amount space required for the full data HashMap

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

@@ -50,7 +50,7 @@ public class PositionCovariate implements Covariate {
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
     public final Comparable getValue( final String str ) {
-        return (int)Integer.parseInt( str ); // cast to primitive int (as opposed to Integer Object) is required so that the return value from the two getValue methods hash to same thing
+        return Integer.parseInt( str );
     }
 
     // Used to estimate the amount space required for the full data HashMap

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

@@ -52,7 +52,7 @@ public class PrimerRoundCovariate implements Covariate {
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
     public final Comparable getValue( final String str ) {
-        return (int)Integer.parseInt( str ); // cast to primitive int (as opposed to Integer Object) is required so that the return value from the two getValue methods hash to same thing
+        return Integer.parseInt( str );
     }
 
     // Used to estimate the amount space required for the full data HashMap

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

@@ -46,7 +46,7 @@ public class QualityScoreCovariate implements Covariate {
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
     public final Comparable getValue( final String str ) {
-        return (int)Integer.parseInt( str ); // cast to primitive int (as opposed to Integer Object) is required so that the return value from the two getValue methods hash to same thing
+        return Integer.parseInt( str );
     }
 
     // Used to estimate the amount space required for the full data HashMap