@Override public VariantAvroFilters addTypeFilter(String type) { return addTypeFilter(VariantType.valueOf(type)); }
public static AlternateCoordinate getAlternateCoordinate(String s) { String[] split = s.split(ALTERNATE_COORDINATE_SEPARATOR, 5); int idx = split[4].lastIndexOf(ALTERNATE_COORDINATE_SEPARATOR); String alternate = split[4].substring(0, idx); VariantType type = VariantType.valueOf(split[4].substring(idx + 1)); return new AlternateCoordinate( split[0], Integer.parseInt(split[1]), Integer.parseInt(split[2]), split[3], alternate, type ); }
public static VariantType getVariantType(VariantProto.VariantType type) { if (type == null) { return null; } switch (type) { case SNV: return VariantType.SNV; case SNP: return VariantType.SNP; case MNV: return VariantType.MNV; case MNP: return VariantType.MNP; case INDEL: return VariantType.INDEL; case SV: return VariantType.SV; case INSERTION: return VariantType.INSERTION; case DELETION: return VariantType.DELETION; case TRANSLOCATION: return VariantType.TRANSLOCATION; case INVERSION: return VariantType.INVERSION; case CNV: return VariantType.CNV; case NO_VARIATION: return VariantType.NO_VARIATION; case SYMBOLIC: return VariantType.SYMBOLIC; case MIXED: return VariantType.MIXED; default: return VariantType.valueOf(type.name()); } }
@Override public Variant convert(ResultSet resultSet) { Variant variant = extractVariantFromResultSet(resultSet); try { String type = resultSet.getString(VariantPhoenixHelper.VariantColumn.TYPE.column()); if (StringUtils.isNotBlank(type)) { variant.setType(VariantType.valueOf(type)); } VariantAnnotation annotation = annotationConverter.convert(resultSet); Map<Integer, StudyEntry> samplesData = studyEntryConverter.convert(resultSet); return convert(variant, samplesData, annotation); } catch (RuntimeException | SQLException e) { logger.error("Fail to parse variant: " + variant); throw Throwables.propagate(e); } } }
builder.setType(VariantType.valueOf(type));
public Set<String> checkArchiveTableLoadedVariants(StudyConfiguration studyConfiguration, VariantHadoopDBAdaptor dbAdaptor, VariantFileMetadata fileMetadata) { int fileId = Integer.valueOf(fileMetadata.getId()); Set<String> variants = getVariants(dbAdaptor, studyConfiguration, fileId); int expected = fileMetadata.getStats().getVariantTypeCounts().entrySet().stream() .filter(entry -> VARIANT_TYPES.contains(VariantType.valueOf(entry.getKey()))) .map(Map.Entry::getValue) .reduce(Integer::sum) .orElse(0); assertEquals(expected, variants.size()); return variants; }
public static AlternateCoordinate convertToAlternateCoordinate(Document alternateDocument) { VariantType variantType = null; String type = (String) alternateDocument.get(ALTERNATES_TYPE); if (type != null && !type.isEmpty()) { variantType = VariantType.valueOf(type); } return new AlternateCoordinate( (String) alternateDocument.get(ALTERNATES_CHR), (Integer) alternateDocument.get(ALTERNATES_START), (Integer) alternateDocument.get(ALTERNATES_END), (String) alternateDocument.get(ALTERNATES_REF), (String) alternateDocument.get(ALTERNATES_ALT), variantType); }
variant.setType(VariantType.valueOf(variantSearchModel.getType()));
VariantType type = VariantType.valueOf(s); Set<VariantType> subTypes = Variant.subTypes(type); ArrayList<VariantType> types = new ArrayList<>(subTypes.size() + 1);
variant.setStudies(studyEntryList); variant.setStrand(strand); variant.setType(VariantType.valueOf(variantType)); variant.setAnnotation(null); variant.setHgvs(null);
if (SKIPPED_VARIANTS.contains(VariantType.valueOf(entry.getKey()))) { expectedSkippedVariants += entry.getValue(); } else {
addQueryFilter(DocumentToVariantConverter.TYPE_FIELD, query.getString(TYPE.key()), builder, QueryOperation.AND, s -> { Set<VariantType> subTypes = Variant.subTypes(VariantType.valueOf(s)); List<String> types = new ArrayList<>(subTypes.size() + 1); types.add(s);
variant.setType(VariantType.valueOf(object.get(TYPE_FIELD).toString()));