diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 8ef032f35..1fae7a85a 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.vcf; +package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broad.tribble.vcf.VCFHeader; import org.broad.tribble.vcf.VCFHeaderLine; @@ -48,7 +48,7 @@ import java.util.*; * priority list (if provided), emits a single record instance at every position represented in the rods. */ @Requires(value={}) -public class VCFCombine extends RodWalker { +public class CombineVariants extends RodWalker { // the types of combinations we currently allow public enum ComboType { UNION, MERGE } @Argument(fullName="combination_type", shortName="type", doc="combination type; MERGE are supported", required=true) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVCF.java index c30dc1ee2..c644dda39 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVCF.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVCF.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.vcf; +package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -39,7 +39,7 @@ import java.util.List; * Filters a lifted-over VCF file for ref bases that have been changed. */ @Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFRecord.class)) -public class FilterLiftedVCF extends RodWalker { +public class FilterLiftedVariants extends RodWalker { private VCFWriter writer; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVCF.java index d2700f1a4..ca13b5bf6 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVCF.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVCF.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.vcf; +package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter; @@ -46,7 +46,7 @@ import net.sf.samtools.SAMFileReader; * Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted. */ @Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFRecord.class)) -public class LiftoverVCF extends RodWalker { +public class LiftoverVariants extends RodWalker { @Argument(fullName="chain", shortName="chain", doc="Chain file", required=true) protected File CHAIN = null;