htsjdk.variant.vcf.VCFFormatHeaderLine Java Examples

/**
 * Does the VCF file use genotype qualities?
 * @param vcfReader
 * @return
 */
public static boolean GQInHeader (final VCFFileReader vcfReader) {
	Collection<VCFFormatHeaderLine> r = vcfReader.getFileHeader().getFormatHeaderLines();
	for (VCFFormatHeaderLine l : r) {
		String id = l.getID();
		if (id.equals("GQ")) return true;
	}
	return false;
}
 

private void addAdditionalHeaderFields(VCFHeader header) {
    header.addMetaDataLine(new VCFHeaderLine(InfiniumVcfFields.ZCALL_VERSION, ZCALL_VERSION));
    header.addMetaDataLine(new VCFHeaderLine(InfiniumVcfFields.ZCALL_THRESHOLDS, ZCALL_THRESHOLDS_FILE.getName()));
    header.addMetaDataLine(new VCFInfoHeaderLine(InfiniumVcfFields.ZTHRESH_X, 1, VCFHeaderLineType.Float, "zCall X threshold"));
    header.addMetaDataLine(new VCFInfoHeaderLine(InfiniumVcfFields.ZTHRESH_Y, 1, VCFHeaderLineType.Float, "zCall Y threshold"));
    header.addMetaDataLine(new VCFFormatHeaderLine(InfiniumVcfFields.GTA, 1, VCFHeaderLineType.String, "Illumina Autocall Genotype"));
    header.addMetaDataLine(new VCFFormatHeaderLine(InfiniumVcfFields.GTZ, 1, VCFHeaderLineType.String, "zCall Genotype"));
}
 

private static File createInputVCF(final String sampleName) {
    final String contig = "chr20";
    final SAMSequenceDictionary dict = new SAMSequenceDictionary(
            Collections.singletonList(new SAMSequenceRecord(contig, 64444167)));

    final VCFFormatHeaderLine formatField = new VCFFormatHeaderLine(SAMPLE_NAME_KEY, 1, VCFHeaderLineType.String,
                                                                    "the name of the sample this genotype came from");
    final Set<VCFHeaderLine> headerLines = new HashSet<>();
    headerLines.add(formatField);
    headerLines.add(new VCFFormatHeaderLine(ANOTHER_ATTRIBUTE_KEY, 1, VCFHeaderLineType.Integer, "Another value"));
    headerLines.add(VCFStandardHeaderLines.getFormatLine("GT"));

    final File out = createTempFile(sampleName +"_", ".vcf");
    try (final VariantContextWriter writer = GATKVariantContextUtils.createVCFWriter(out.toPath(), dict, false,
                                                                                     Options.INDEX_ON_THE_FLY)) {
        final VCFHeader vcfHeader = new VCFHeader(headerLines, Collections.singleton(sampleName));
        vcfHeader.setSequenceDictionary(dict);
        writer.writeHeader(vcfHeader);
        final Allele Aref = Allele.create("A", true);
        final Allele C = Allele.create("C");
        final List<Allele> alleles = Arrays.asList(Aref, C);
        final VariantContext variant = new VariantContextBuilder("invented", contig, INTERVAL.get(0).getStart(), INTERVAL.get(0).getStart(), alleles)
                .genotypes(new GenotypeBuilder(sampleName, alleles).attribute(SAMPLE_NAME_KEY, sampleName)
                                   .attribute(ANOTHER_ATTRIBUTE_KEY, 10).make())
                .make();
        writer.add(variant);
        return out;
    }
}
 

private static boolean parseOtherGenotypeFields(String field, VariantContext vc,
    ListValue.Builder lvBuilder, Genotype g, VCFHeader header) {

  if (!g.hasAnyAttribute(field)) {
    return false;
  }

  final VCFFormatHeaderLine metaData = header.getFormatHeaderLine(field);
  if (metaData == null) {
    logger.log(Level.WARNING, String.format("Could not find matching VCF header field for "
        + "genotype field %s", field));
    return false;
  }

  VCFHeaderLineType type = metaData.getType();
  Object value = g.getExtendedAttribute(field);
  final int fieldCount = metaData.getCount(vc);
  if (fieldCount == 1) {
    lvBuilder.addValues(createTypedValue(type, value));
    return true;
  }

  if (!(value instanceof String)) {
    throw new IllegalStateException("received non-Flag genotype field as non-String type");
  }
  String[] valueArray = ((String) value).split(",");
  if (valueArray.length == 1) {
    throw new IllegalStateException(String.format("header indicating a count greater than 1 "
        + "with non-List type found for field %s",
        field));
  }

  boolean allFalse = true;
  for (int i = 0; i < valueArray.length; i++) {
    VCFHeaderLineType thisType = VCFHeaderLineType.String;
    if (!valueArray[i].equals(VCFConstants.MISSING_VALUE_v4)) {
      thisType = type;
      allFalse = false;
    }

    lvBuilder.addValues(createTypedValue(thisType, valueArray[i]));
  }
  // We only add the lvBuilder if there is at least one non-missing value
  return !allFalse;
}
 

@Override
public List<VCFFormatHeaderLine> getDescriptions() {
    return Arrays.asList(new VCFFormatHeaderLine(POSTERIOR_PROBABILITIES_KEY, 3, VCFHeaderLineType.Float, "posterior probabilities of the presence of strand artifact"),
            new VCFFormatHeaderLine(MAP_ALLELE_FRACTIONS_KEY, 3, VCFHeaderLineType.Float, "MAP estimates of allele fraction given z"));
}
 

@Override
public List<VCFFormatHeaderLine> getDescriptions() {
    return Arrays.asList(new VCFFormatHeaderLine(getVcfKey(), VCFHeaderLineCount.A, VCFHeaderLineType.Float, getDescription()));
}
 

@Override
public List<VCFFormatHeaderLine> getDescriptions() {
    return Collections.singletonList(VCFStandardHeaderLines.getFormatLine(getKeyNames().get(0)));
}
 

@Override
public List<VCFFormatHeaderLine> getDescriptions() {
    return Collections.singletonList(GATKVCFHeaderLines.getFormatLine(getKeyNames().get(0)));
}
 

@Override
public List<VCFFormatHeaderLine> getDescriptions() {
    return Collections.singletonList(GATKVCFHeaderLines.getFormatLine(getKeyNames().get(0)));
}
 

@Override
public List<VCFFormatHeaderLine> getDescriptions() {
    return Collections.singletonList(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY));
}
 

@Override
public List<VCFFormatHeaderLine> getDescriptions() {
    return Arrays.asList(
            GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.F1R2_KEY),
            GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.F2R1_KEY));
}
 

/**
 * Return the descriptions used for the VCF FORMAT meta field.
 * Subclasses must ensure that this list is not null and does not contain null.
 */
public abstract List<VCFFormatHeaderLine> getDescriptions();