diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java index 99a4ad787..3819ce354 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java +++ b/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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java index 3ff9a5b8f..9552b7842 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java +++ b/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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java index 7f8f39143..505f6be8d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java +++ b/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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java index 60f66516e..0742f2a8c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java +++ b/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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java index 78a965cc2..0a668c810 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java +++ b/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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java index a90458c5d..c9123e4ab 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java +++ b/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