gatk-3.8/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java

package org.broadinstitute.sting.gatk.walkers;

import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.genotype.vcf.*;
import org.broadinstitute.sting.utils.BaseUtils;

import java.util.*;

/**
 * Converts variants from other file formats to VCF format.
 */
@Requires(value={},referenceMetaData=@RMD(name=VariantsToVCF.INPUT_ROD_NAME,type= ReferenceOrderedDatum.class))
public class VariantsToVCF extends RodWalker<Integer, Integer> {

    public static final String INPUT_ROD_NAME = "variant";

    @Argument(fullName="sample", shortName="sample", doc="The sample name represented by the variant rod (for data like GELI with genotypes)", required=false)
    protected String sampleName = null;

    private VCFWriter vcfwriter = null;

    // Don't allow mixed types for now
    private EnumSet<VariantContext.Type> ALLOWED_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP, VariantContext.Type.NO_VARIATION, VariantContext.Type.INDEL);

    private String[] ALLOWED_FORMAT_FIELDS = {"GT"};

    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
        if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )
            return 0;

        rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData("dbsnp"));

        Allele refAllele = new Allele(Character.toString(ref.getBase()), true);
        Collection<VariantContext> contexts = tracker.getVariantContexts(INPUT_ROD_NAME, ALLOWED_VARIANT_CONTEXT_TYPES, context.getLocation(), refAllele, true, false);

        for ( VariantContext vc : contexts ) {
            VCFRecord vcf = VariantContextAdaptors.toVCF(vc, ref.getBase(), Arrays.asList(ALLOWED_FORMAT_FIELDS), false, false);
            if ( dbsnp != null )
                vcf.setID(dbsnp.getRS_ID());
            // set the appropriate sample name if necessary
            if ( sampleName != null && vcf.hasGenotypeData() && vcf.getGenotype(INPUT_ROD_NAME) != null )
                 vcf.getGenotype(INPUT_ROD_NAME).setSampleName(sampleName);
            writeRecord(vcf, tracker);
        }

        return 1;
    }

    private void writeRecord(VCFRecord rec, RefMetaDataTracker tracker) {
        if ( vcfwriter == null ) {
            // setup the header fields
            Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
            hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
            hInfo.add(new VCFHeaderLine("source", "VariantsToVCF"));
            hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));

            TreeSet<String> samples = new TreeSet<String>();
            if ( sampleName != null ) {
                samples.add(sampleName);
            } else {

                List<Object> rods = tracker.getReferenceMetaData(INPUT_ROD_NAME);
                if ( rods.size() == 0 )
                    throw new IllegalStateException("VCF record was created, but no rod data is present");

                Object rod = rods.get(0);
                if ( rod instanceof RodVCF )
                    samples.addAll(Arrays.asList(((RodVCF)rod).getSampleNames()));
                else if ( rod instanceof HapMapROD )
                    samples.addAll(Arrays.asList(((HapMapROD)rod).getSampleIDs()));
                else
                    samples.addAll(Arrays.asList(rec.getSampleNames()));
            }

            vcfwriter = new VCFWriter(out);
            vcfwriter.writeHeader(new VCFHeader(hInfo, samples));
        }
        vcfwriter.addRecord(rec);
    }

    public Integer reduceInit() {
        return 0;
    }

    public Integer reduce(Integer value, Integer sum) {
        return value + sum;
    }

    public void onTraversalDone(Integer sum) {
        if ( vcfwriter != null )
            vcfwriter.close();
    }
}