VariantFileMetadata() { impl = new org.opencb.biodata.models.variant.metadata.VariantFileMetadata(); samplesPosition = null; }
public VariantFileMetadata(String id, String path, List<String> sampleIds, org.opencb.biodata.models.variant.metadata.VariantSetStats stats, VariantFileHeader header) { impl = new org.opencb.biodata.models.variant.metadata.VariantFileMetadata(id, path, sampleIds, stats, header, new HashMap<>()); samplesPosition = null; }
/** * 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); }
@Override public VariantFileMetadata build() { try { VariantFileMetadata record = new VariantFileMetadata(); record.id = fieldSetFlags()[0] ? this.id : (java.lang.String) defaultValue(fields()[0]); record.path = fieldSetFlags()[1] ? this.path : (java.lang.String) defaultValue(fields()[1]); record.sampleIds = fieldSetFlags()[2] ? this.sampleIds : (java.util.List<java.lang.String>) defaultValue(fields()[2]); record.stats = fieldSetFlags()[3] ? this.stats : (org.opencb.biodata.models.variant.metadata.VariantSetStats) defaultValue(fields()[3]); record.header = fieldSetFlags()[4] ? this.header : (org.opencb.biodata.models.variant.metadata.VariantFileHeader) defaultValue(fields()[4]); record.attributes = fieldSetFlags()[5] ? this.attributes : (java.util.Map<java.lang.String,java.lang.String>) defaultValue(fields()[5]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }