@Deprecated public void setAttributes(Map<String, String> attributes) { if (impl.getFiles().isEmpty()) { impl.getFiles().add(new FileEntry("", null, attributes)); } else { impl.getFiles().get(0).setAttributes(attributes); } }
fe.setAttributes(feAttr);
fileEntry.setCall(fileInfoAttributes.get("fileCall")); fileInfoAttributes.remove("fileCall"); fileEntry.setAttributes(fileInfoAttributes);
studyEntry.getFile(fileEntry.getFileId()).setAttributes(fileEntry.getAttributes());
public Variant convert(VcfSliceProtos.VcfRecord vcfRecord, String chromosome, int slicePosition) { int start = getStart(vcfRecord, slicePosition); int end = getEnd(vcfRecord, slicePosition); Variant variant = new Variant(chromosome, start, end, vcfRecord.getReference(), vcfRecord.getAlternate()); variant.setType(getVariantType(vcfRecord.getType())); variant.setIds(vcfRecord.getIdNonDefaultList()); variant.resetLength(); FileEntry fileEntry = new FileEntry(); fileEntry.setFileId(fileId); Map<String, String> attributes = getFileAttributes(vcfRecord); fileEntry.setAttributes(attributes); fileEntry.setCall(vcfRecord.getCall().isEmpty() ? null : vcfRecord.getCall()); if (vcfRecord.getType().equals(VariantProto.VariantType.NO_VARIATION)) { attributes.put("END", Integer.toString(end)); } StudyEntry studyEntry = new StudyEntry(studyId); studyEntry.setFiles(Collections.singletonList(fileEntry)); studyEntry.setFormat(getFormat(vcfRecord)); studyEntry.setSamplesData(getSamplesData(vcfRecord, studyEntry.getFormatPositions())); studyEntry.setSamplesPosition(retrieveSamplePosition()); studyEntry.getFormatPositions(); // Initialize the map List<VariantProto.AlternateCoordinate> alts = vcfRecord.getSecondaryAlternatesList(); studyEntry.setSecondaryAlternates(getAlternateCoordinates(alts)); variant.addStudyEntry(studyEntry); studyEntry.getFormatPositions(); // Initialize the map return variant; }