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davidbenjamin committed May 5, 2021
1 parent 82ec5fb commit 1b74432
Showing 1 changed file with 15 additions and 4 deletions.
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import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.vcf.VCFStandardHeaderLines;
import htsjdk.variant.vcf.*;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.engine.ReferenceContext;
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return allKeys;
}

@Override
public List<VCFCompoundHeaderLine> getDescriptions() {
return Arrays.asList(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0)));
}

@Override
public List<VCFCompoundHeaderLine> getRawDescriptions() {
final List<VCFCompoundHeaderLine> lines = new ArrayList<>(1);
for (final String rawKey : getRawKeyNames()) {
lines.add(GATKVCFHeaderLines.getInfoLine(rawKey));
}
return lines;
}

/**
* Generate the raw data necessary to calculate the annotation. Raw data is the final endpoint for gVCFs.
*/
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