.collect(Collectors.toMap(VariantFileHeaderSimpleLine::getKey, VariantFileHeaderSimpleLine::getValue)); header.getSimpleLines().forEach((line) -> { String oldValue = simpleLines.put(line.getKey(), line.getValue()); if (oldValue != null && !oldValue.equals(line.getValue())) { simpleLines.put(line.getKey(), UNKNOWN_HEADER_ATTRIBUTE); this.variantHeader.setSimpleLines(simpleLines.entrySet() .stream() .map(e -> new VariantFileHeaderSimpleLine(e.getKey(), e.getValue())) .collect(Collectors.toList()));
@Override public List<VS> apply(List<VariantFileMetadata> variantFileMetadata) { Set<VS> gaVariantSets = new LinkedHashSet<>(); for (VariantFileMetadata fileMetadata : variantFileMetadata) { List<Object> metadata = new ArrayList<>(); for (VariantFileHeaderComplexLine line : fileMetadata.getHeader().getComplexLines()) { Map<String, List<String>> info = line.getGenericFields().entrySet().stream() .collect(Collectors.toMap(Map.Entry::getKey, value -> Arrays.asList(value.getValue().split(",")))); metadata.add(factory.newVariantSetMetadata(line.getKey(), null, line.getId(), line.getType(), line.getNumber(), line.getDescription(), info)); } fileMetadata.getHeader().getSimpleLines().forEach(line -> metadata.add(factory.newVariantSetMetadata(line.getKey(), line.getValue(), null, null, null, null, Collections.emptyMap()))); @SuppressWarnings("unchecked") VS variantSet = (VS) factory.newVariantSet(fileMetadata.getId(), fileMetadata.getPath(), "", "", (List) metadata); gaVariantSets.add(variantSet); } return new ArrayList<>(gaVariantSets); }
@Override public VariantFileHeaderSimpleLine build() { try { VariantFileHeaderSimpleLine record = new VariantFileHeaderSimpleLine(); record.key = fieldSetFlags()[0] ? this.key : (java.lang.String) defaultValue(fields()[0]); record.value = fieldSetFlags()[1] ? this.value : (java.lang.String) defaultValue(fields()[1]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }
List<VariantFileHeaderSimpleLine> headerSimpleLines = new ArrayList<>(studyHeader.getSimpleLines().size()); studyHeader.getSimpleLines().forEach(line -> { if (!StudyConfiguration.UNKNOWN_HEADER_ATTRIBUTE.equals(line.getValue())) { headerSimpleLines.add(line);
for (Object value : values) { if (value instanceof String) { variantFileHeader.getSimpleLines().add(new VariantFileHeaderSimpleLine(key, ((String) value))); } else if (value instanceof Map) { Map<String, String> map = (Map<String, String>) value;
simpleLines.add(new VariantFileHeaderSimpleLine(line.getKey(), line.getValue()));