public VariantFileMetadata setHeader(VariantFileHeader header) { impl.setHeader(header); return this; }
/** * Add a variant file metadata (from VCF file and header) to a given variant study metadata (from study ID). * * @param filename VCF filename (as an ID) * @param vcfHeader VCF header * @param studyId Study ID */ public void addFile(String filename, VCFHeader vcfHeader, String studyId) { // sanity check if (StringUtils.isEmpty(filename)) { logger.error("VCF filename is empty or null: '{}'", filename); return; } if (vcfHeader == null) { logger.error("VCF header is missingDataset not found. Check your study ID: '{}'", studyId); return; } VCFHeaderToVariantFileHeaderConverter headerConverter = new VCFHeaderToVariantFileHeaderConverter(); VariantFileMetadata variantFileMetadata = new VariantFileMetadata(); variantFileMetadata.setId(filename); variantFileMetadata.setSampleIds(vcfHeader.getSampleNamesInOrder()); variantFileMetadata.setHeader(headerConverter.convert(vcfHeader)); addFile(variantFileMetadata, studyId); }