private static Set<VCFHeaderLine> makeGetMetaDataSet(final Set<VCFHeaderLine> headerLinesInSomeOrder) { final Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>(); lines.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_2.getFormatString(), VCFHeaderVersion.VCF4_2.getVersionString())); lines.addAll(headerLinesInSomeOrder); return Collections.unmodifiableSet(lines); }
private static Set<VCFHeaderLine> makeGetMetaDataSet(final Set<VCFHeaderLine> headerLinesInSomeOrder) { final Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>(); lines.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_2.getFormatString(), VCFHeaderVersion.VCF4_2.getVersionString())); lines.addAll(headerLinesInSomeOrder); return Collections.unmodifiableSet(lines); }
private static Set<VCFHeaderLine> makeGetMetaDataSet(final Set<VCFHeaderLine> headerLinesInSomeOrder) { final Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>(); lines.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_1.getFormatString(), VCFHeaderVersion.VCF4_1.getVersionString())); lines.addAll(headerLinesInSomeOrder); return Collections.unmodifiableSet(lines); }
/** * create a fake header of known quantity * @param metaData the header lines * @param additionalColumns the additional column names * @return a fake VCF header */ private static VCFHeader createFakeHeader(final Set<VCFHeaderLine> metaData, final Set<String> additionalColumns, final SAMSequenceDictionary sequenceDict) { metaData.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_0.getFormatString(), VCFHeaderVersion.VCF4_0.getVersionString())); metaData.add(new VCFHeaderLine("two", "2")); additionalColumns.add("extra1"); additionalColumns.add("extra2"); final VCFHeader ret = new VCFHeader(metaData, additionalColumns); ret.setSequenceDictionary(sequenceDict); return ret; }
public void writeAsVcf(final File output, final File refFile) throws FileNotFoundException { ReferenceSequenceFile ref = new IndexedFastaSequenceFile(refFile); try (VariantContextWriter writer = new VariantContextWriterBuilder() .setOutputFile(output) .setReferenceDictionary(ref.getSequenceDictionary()) .build()) { final VCFHeader vcfHeader = new VCFHeader( VCFUtils.withUpdatedContigsAsLines(Collections.emptySet(), refFile, header.getSequenceDictionary(), false), Collections.singleton(HET_GENOTYPE_FOR_PHASING)); VCFUtils.withUpdatedContigsAsLines(Collections.emptySet(), refFile, header.getSequenceDictionary(), false); vcfHeader.addMetaDataLine(new VCFHeaderLine(VCFHeaderVersion.VCF4_2.getFormatString(), VCFHeaderVersion.VCF4_2.getVersionString())); vcfHeader.addMetaDataLine(new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed")); vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype")); vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.PHASE_SET_KEY, 1, VCFHeaderLineType.String, "Phase-set identifier for phased genotypes.")); vcfHeader.addMetaDataLine(new VCFHeaderLine(VCFHeader.SOURCE_KEY,"HaplotypeMap::writeAsVcf")); vcfHeader.addMetaDataLine(new VCFHeaderLine("reference","HaplotypeMap::writeAsVcf")); // vcfHeader.addMetaDataLine(new VCFHeaderLine()); writer.writeHeader(vcfHeader); final LinkedList<VariantContext> variants = new LinkedList<>(this.asVcf(ref)); variants.sort(vcfHeader.getVCFRecordComparator()); variants.forEach(writer::add); } }
public void writeAsVcf(final File output, final File refFile) throws FileNotFoundException { ReferenceSequenceFile ref = new IndexedFastaSequenceFile(refFile); try (VariantContextWriter writer = new VariantContextWriterBuilder() .setOutputFile(output) .setReferenceDictionary(ref.getSequenceDictionary()) .build()) { final VCFHeader vcfHeader = new VCFHeader( VCFUtils.withUpdatedContigsAsLines(Collections.emptySet(), refFile, header.getSequenceDictionary(), false), Collections.singleton(HET_GENOTYPE_FOR_PHASING)); VCFUtils.withUpdatedContigsAsLines(Collections.emptySet(), refFile, header.getSequenceDictionary(), false); vcfHeader.addMetaDataLine(new VCFHeaderLine(VCFHeaderVersion.VCF4_2.getFormatString(), VCFHeaderVersion.VCF4_2.getVersionString())); vcfHeader.addMetaDataLine(new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed")); vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype")); vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.PHASE_SET_KEY, 1, VCFHeaderLineType.String, "Phase-set identifier for phased genotypes.")); vcfHeader.addMetaDataLine(new VCFHeaderLine(VCFHeader.SOURCE_KEY,"HaplotypeMap::writeAsVcf")); vcfHeader.addMetaDataLine(new VCFHeaderLine("reference","HaplotypeMap::writeAsVcf")); // vcfHeader.addMetaDataLine(new VCFHeaderLine()); writer.writeHeader(vcfHeader); final LinkedList<VariantContext> variants = new LinkedList<>(this.asVcf(ref)); variants.sort(vcfHeader.getVCFRecordComparator()); variants.forEach(writer::add); } }