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*facepalm* 

forgot to add the samples to the header. How could the VCFWriter let me get away with something so boneheaded?!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4513 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-10-17 05:36:29 +00:00
parent e6d038067b
commit 5889138f4a
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java
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@ -17,6 +17,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import java.util.*;
@ -34,9 +35,10 @@ public class FixRefBases extends RodWalker<Integer,Integer> {
public void initialize() {
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("variant"));
Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger);
headerLines.add(new VCFHeaderLine("source", "SelectVariants"));
out.writeHeader(new VCFHeader(headerLines));
out.writeHeader(new VCFHeader(headerLines,vcfSamples));
}
public Integer reduceInit() {