throw new IllegalArgumentException("Sequence dictionary was missing or empty for the VCF: " + input.getAbsolutePath() + " Please add a sequence dictionary to this VCF or specify SEQUENCE_DICTIONARY."); header.setSequenceDictionary(samSequenceDictionary); } else { if (null == samSequenceDictionary) {
private static VariantContextWriter getVariantContextWriter(final File outputFile, final File referenceSequenceFileName, final String sample, final String source, final ReferenceSequenceFile ref) { final VariantContextWriter variantContextWriter = new VariantContextWriterBuilder() .setReferenceDictionary(ref.getSequenceDictionary()) .setOutputFile(outputFile).build(); final Set<VCFHeaderLine> lines = new LinkedHashSet<>(); lines.add(new VCFHeaderLine("reference", referenceSequenceFileName.getAbsolutePath())); lines.add(new VCFHeaderLine("source", source)); lines.add(new VCFHeaderLine("fileDate", new Date().toString())); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_PL_KEY)); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS)); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY)); final VCFHeader header = new VCFHeader(lines, Collections.singletonList(sample)); header.setSequenceDictionary(ref.getSequenceDictionary()); variantContextWriter.writeHeader(header); return variantContextWriter; }
throw new IllegalArgumentException("Sequence dictionary was missing or empty for the VCF: " + input.getAbsolutePath() + " Please add a sequence dictionary to this VCF or specify SEQUENCE_DICTIONARY."); header.setSequenceDictionary(samSequenceDictionary); } else { if (null == samSequenceDictionary) {
private static VariantContextWriter getVariantContextWriter(final File outputFile, final File referenceSequenceFileName, final String sample, final String source, final ReferenceSequenceFile ref) { final VariantContextWriter variantContextWriter = new VariantContextWriterBuilder() .setReferenceDictionary(ref.getSequenceDictionary()) .setOutputFile(outputFile).build(); final Set<VCFHeaderLine> lines = new LinkedHashSet<>(); lines.add(new VCFHeaderLine("reference", referenceSequenceFileName.getAbsolutePath())); lines.add(new VCFHeaderLine("source", source)); lines.add(new VCFHeaderLine("fileDate", new Date().toString())); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_PL_KEY)); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS)); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY)); final VCFHeader header = new VCFHeader(lines, Collections.singletonList(sample)); header.setSequenceDictionary(ref.getSequenceDictionary()); variantContextWriter.writeHeader(header); return variantContextWriter; }
/** * create a fake header of known quantity * @param metaData the header lines * @param additionalColumns the additional column names * @return a fake VCF header */ public static VCFHeader createFakeHeader(final Set<VCFHeaderLine> metaData, final Set<String> additionalColumns, final SAMSequenceDictionary sequenceDict) { metaData.add(new VCFHeaderLine("two", "2")); additionalColumns.add("extra1"); additionalColumns.add("extra2"); final VCFHeader ret = new VCFHeader(metaData, additionalColumns); ret.setSequenceDictionary(sequenceDict); return ret; }
/** * Gets a VCF file ready to write variants to * A header based on this processing context will have already been written to the returned writer * It is the responsibility of the caller to close the returned @link {@link VariantContextWriter} * @param output file * @return opened output VCF stream */ @Override public VariantContextWriter getVariantContextWriter(File file, boolean createIndex) { VariantContextWriterBuilder builder = getVariantContextWriterBuilder(file, createIndex); VariantContextWriter vcfWriter = builder.build(); final VCFHeader vcfHeader = new VCFHeader(Collections.emptySet(), categories); GridssVcfConstants.addHeaders(vcfHeader); vcfHeader.setSequenceDictionary(getReference().getSequenceDictionary()); vcfWriter.writeHeader(vcfHeader); return vcfWriter; } public EvidenceIdentifierGenerator getEvidenceIDGenerator() {
/** * 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; }
/** * Gets a VCF file ready to write variants to * A header based on this processing context will have already been written to the returned writer * It is the responsibility of the caller to close the returned @link {@link VariantContextWriter} * @param output file * @return opened output VCF stream */ public VariantContextWriter getVariantContextWriter(File file, VCFHeader vcfHeader, boolean createIndex) { VariantContextWriterBuilder builder = getVariantContextWriterBuilder(file, createIndex); VariantContextWriter vcfWriter = builder.build(); GridssVcfConstants.addHeaders(vcfHeader); vcfHeader.setSequenceDictionary(getReference().getSequenceDictionary()); vcfWriter.writeHeader(vcfHeader); return vcfWriter; } /**
throw new IllegalArgumentException(SEQ_DICT_REQUIRED); } else { fileHeader.setSequenceDictionary(sequenceDictionary);
throw new IllegalArgumentException(SEQ_DICT_REQUIRED); } else { fileHeader.setSequenceDictionary(sequenceDictionary);
/** * create a fake header of known quantity * * @return a fake VCF header */ private static VCFHeader createFakeHeader() { final SAMSequenceDictionary sequenceDict = createArtificialSequenceDictionary(); final Set<VCFHeaderLine> metaData = new HashSet<>(); final Set<String> additionalColumns = new HashSet<>(); metaData.add(new VCFHeaderLine("two", "2")); additionalColumns.add("extra1"); additionalColumns.add("extra2"); final VCFHeader header = new VCFHeader(metaData, additionalColumns); header.addMetaDataLine(new VCFInfoHeaderLine("DP", 1, VCFHeaderLineType.String, "x")); header.addMetaDataLine(new VCFFormatHeaderLine("GT", 1, VCFHeaderLineType.String, "x")); header.addMetaDataLine(new VCFFormatHeaderLine("BB", 1, VCFHeaderLineType.String, "x")); header.addMetaDataLine(new VCFFormatHeaderLine("GQ", 1, VCFHeaderLineType.String, "x")); header.setSequenceDictionary(sequenceDict); return header; }
fileHeader.setSequenceDictionary(samSequenceDictionary); vcfWriter.writeHeader(fileHeader);
fileHeader.setSequenceDictionary(samSequenceDictionary); vcfWriter.writeHeader(fileHeader);
outHeader.setSequenceDictionary(walker.getSequenceDictionary()); if (WRITE_ORIGINAL_POSITION) { for (final VCFInfoHeaderLine line : ATTRS) outHeader.addMetaDataLine(line);
outHeader.setSequenceDictionary(walker.getSequenceDictionary()); if (WRITE_ORIGINAL_POSITION) { for (final VCFInfoHeaderLine line : ATTRS) outHeader.addMetaDataLine(line);