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Minor fix for missing INFO key definition in VCF header

This commit is contained in:
Geraldine Van der Auwera 2014-10-21 15:21:12 -04:00
parent edaa78dea1
commit 895b8c5931
1 changed files with 6 additions and 7 deletions
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13
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java
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@ -51,6 +51,7 @@
package org.broadinstitute.gatk.tools.walkers.validation;
import htsjdk.variant.vcf.*;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.walkers.*;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider;
@ -64,13 +65,10 @@ import org.broadinstitute.gatk.utils.SampleUtils;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.VCFUtils;
import java.util.Map;
import java.util.Set;
@ -80,6 +78,8 @@ import static org.broadinstitute.gatk.utils.IndelUtils.isInsideExtendedIndel;
/**
* Genotypes a dataset and validates the calls of another dataset using the Unified Genotyper.
*
* <h4>Note that this is an old tool that makes use of the UnifiedGenotyper, which has since been
* deprecated in favor of the HaplotypeCaller.</h4>
* <p>
* Genotype and Validate is a tool to evaluate the quality of a dataset for calling SNPs
* and Indels given a secondary (validation) data source. The data sources are BAM or VCF
@ -212,9 +212,6 @@ import static org.broadinstitute.gatk.utils.IndelUtils.isInsideExtendedIndel;
* -o gav.vcf
* </pre>
*
*
* @author Mauricio Carneiro
* @since ${DATE}
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, extraDocs = {CommandLineGATK.class} )
@ -226,8 +223,9 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
/**
* The optional output file that will have all the variants used in the Genotype and Validation essay.
* The new annotation `callStatus` will carry the value called in the validation VCF or BAM file."
*/
@Output(doc="Generate a VCF file with the variants considered by the walker, with a new annotation \"callStatus\" which will carry the value called in the validation VCF or BAM file", required=false)
@Output(doc="Output VCF file with annotated variants", required=false)
protected VariantContextWriter vcfWriter = null;
/**
@ -335,6 +333,7 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
samples = SampleUtils.getSampleList(header, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(header.values(), true);
headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate"));
headerLines.add(new VCFInfoHeaderLine("callStatus", 1, VCFHeaderLineType.String, "Value from the validation VCF"));
vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
}