diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java index cec40b5bd..43063da17 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java @@ -104,7 +104,7 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec getFeatureType() { return RefSeqFeature.class; } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java index ab1ac59d8..4e734294f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java @@ -51,7 +51,7 @@ public class TableCodec implements ReferenceDependentFeatureCodec { } @Override - public Class getFeatureType() { + public Class getFeatureType() { return TableFeature.class; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java index fef6c4ea0..c30da828e 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java @@ -117,7 +117,7 @@ public class CGVarCodec implements FeatureCodec { return new VariantContext("CGI", array[3], start, end, alleles, VariantContext.NO_NEG_LOG_10PERROR, null, attrs); } - public Class getFeatureType() { + public Class getFeatureType() { return VariantContext.class; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java index 90878dee7..535f607a1 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java @@ -82,7 +82,7 @@ public class RawHapMapCodec implements FeatureCodec { headerLine); } - public Class getFeatureType() { + public Class getFeatureType() { return RawHapMapFeature.class; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java index eada8521f..b5efb49a7 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java @@ -222,7 +222,7 @@ public class SnpEffCodec implements FeatureCodec, SelfScopingFeatureCodec { return null; } - public Class getFeatureType() { + public Class getFeatureType() { return SnpEffFeature.class; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java index e169dbdfc..284c43e90 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java @@ -178,7 +178,7 @@ public class SoapSNPCodec implements FeatureCodec, NameAwareCodec { /** * @return VariantContext */ - public Class getFeatureType() { + public Class getFeatureType() { return VariantContext.class; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index cb505c717..19f58ddaa 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -263,7 +263,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, * * @return the type of record */ - public Class getFeatureType() { + public Class getFeatureType() { return VariantContext.class; }