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fixing the build 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1546 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-09-08 13:13:55 +00:00
parent f963cfcb21
commit 3276e01e5f
1 changed files with 11 additions and 12 deletions
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23
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java
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@ -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<Integer, Integer> {
@Argument(fullName="vcfout", shortName="VO", doc="The output VCF file") public File VCF_OUT;
@ -84,8 +83,8 @@ public class VariantsToVCF extends RefWalker<Integer, Integer> {
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;
}