diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java index 8cc42dd8b..f27096adb 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java @@ -1,20 +1,19 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantstovcf; -import org.broadinstitute.sting.gatk.walkers.RefWalker; -import org.broadinstitute.sting.gatk.refdata.*; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.*; +import org.broadinstitute.sting.gatk.walkers.RefWalker; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.cmdLine.Argument; +import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord; import org.broadinstitute.sting.utils.genotype.vcf.VCFHeader; import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord; -import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord; -import org.broadinstitute.sting.utils.cmdLine.Argument; -import org.broadinstitute.sting.utils.ListUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter; -import java.util.*; import java.io.File; +import java.util.*; public class VariantsToVCF extends RefWalker { @Argument(fullName="vcfout", shortName="VO", doc="The output VCF file") public File VCF_OUT; @@ -84,8 +83,8 @@ public class VariantsToVCF extends RefWalker { String lod = String.format("%d", av.getVariationConfidence() > 99 ? 99 : (int) av.getVariationConfidence()); int depth = 0; - if (rod instanceof rodVariants) { - rodVariants rv = (rodVariants) rod; + if (rod instanceof RodGeliText) { + RodGeliText rv = (RodGeliText) rod; depth = rv.depth; }