Examples with Family com.github.lindenb.jvarkit.pedigree.Family used on opensource projects

Example 1 with Family

use of com.github.lindenb.jvarkit.pedigree.Family in project jvarkit by lindenb.

the class VCFFamilies method doVcfToVcf.

@Override
public int doVcfToVcf(final String inputName, VCFIterator r, final VariantContextWriter w) {
    final VCFHeader header = r.getHeader();
    final Pedigree pedigree;
    try {
        pedigree = new PedigreeParser().parse(this.pedigreeFile);
    } catch (final Throwable err) {
        throw new RuntimeIOException(err);
    }
    if (pedigree == null || pedigree.isEmpty()) {
        throw new RuntimeIOException("Pedigree null/empty");
    }
    final VCFHeader h2 = new VCFHeader(header);
    final Map<String, FamilyInfo> famidToFamilyInfo = new HashMap<>();
    pedigree.getSamplesInVcfHeader(header).forEach(P -> {
        final Family pedFamily = P.getFamily();
        FamilyInfo finfo = famidToFamilyInfo.get(pedFamily.getId());
        if (finfo == null) {
            finfo = new FamilyInfo(pedFamily);
            famidToFamilyInfo.put(pedFamily.getId(), finfo);
        }
        finfo.samples.add(P.getId());
    });
    famidToFamilyInfo.values().stream().flatMap(F -> F.getMetaDataLines().stream()).forEach(H -> h2.addMetaDataLine(H));
    JVarkitVersion.getInstance().addMetaData(this, h2);
    w.writeHeader(h2);
    while (r.hasNext()) {
        final VariantContext ctx = r.next();
        final VariantContextBuilder vcb = new VariantContextBuilder(ctx);
        final List<Allele> alts = ctx.getAlternateAlleles();
        famidToFamilyInfo.values().forEach(F -> F.visit(vcb, ctx, alts));
        w.add(vcb.make());
    }
    w.close();
    return 0;
}