public int getVariantTypeCount(VariantType key) { return impl.getVariantTypeCounts().getOrDefault(key.toString(), 0); }
@Override public VariantAvroFilters addTypeFilter(String type) { return addTypeFilter(VariantType.valueOf(type)); }
@Override public QueryResult<String> getVariantTypes() { List<String> variantTypes = Arrays.stream(VariantType.values()) .map((value) -> value.name()).collect(Collectors.toList()); QueryResult<String> queryResult = new QueryResult<String>("variant_types", 0, variantTypes.size(), variantTypes.size(), null, null, variantTypes); return queryResult; }
@Override protected void loadTerms(Map<String, String> params, RandomQueries randomQueries) { if (randomQueries.getType() != null && !randomQueries.getType().isEmpty()) { this.terms = randomQueries.getType(); } else { for (VariantType variantType : VariantType.values()) { terms.add(variantType.toString()); } } } }
if (SKIPPED_VARIANTS.contains(VariantType.valueOf(entry.getKey()))) { expectedSkippedVariants += entry.getValue(); } else { logger.warn("There were " + writeResult.getSkippedVariants() + " skipped variants."); for (VariantType type : SKIPPED_VARIANTS) { Integer countByType = fileMetadata.getStats().getVariantTypeCounts().get(type.toString()); if (countByType != null && countByType > 0) { logger.info(" * Of which " + countByType + " are " + type.toString() + " variants.");
public static VariantProto.VariantType getProtoVariantType(VariantType type) { if (type == null) { return null; } switch (type) { case SNV: return VariantProto.VariantType.SNV; case SNP: return VariantProto.VariantType.SNP; case MNV: return VariantProto.VariantType.MNV; case MNP: return VariantProto.VariantType.MNP; case INDEL: return VariantProto.VariantType.INDEL; case SV: return VariantProto.VariantType.SV; case INSERTION: return VariantProto.VariantType.INSERTION; case DELETION: return VariantProto.VariantType.DELETION; case TRANSLOCATION: return VariantProto.VariantType.TRANSLOCATION; case INVERSION: return VariantProto.VariantType.INVERSION; case CNV: return VariantProto.VariantType.CNV; case NO_VARIATION: return VariantProto.VariantType.NO_VARIATION; case SYMBOLIC: return VariantProto.VariantType.SYMBOLIC; case MIXED: return VariantProto.VariantType.MIXED; case DUPLICATION: return VariantProto.VariantType.DUPLICATION; case BREAKEND: return VariantProto.VariantType.BREAKEND; default: throw new EnumConstantNotPresentException(VariantProto.VariantType.class, type.name()); } }
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); subTypes.forEach(subType -> types.add(subType.toString())); return types;
int expectedCount = 0; for (VariantType variantType : TARGET_VARIANT_TYPE_SET) { expectedCount += variantFileMetadata.getStats().getVariantTypeCounts().getOrDefault(variantType.toString(), 0); for (VariantType type : VariantType.values()) { if (!TARGET_VARIANT_TYPE_SET.contains(type)) { Integer countByType = variantFileMetadata.getStats().getVariantTypeCounts().get(type.toString()); if (countByType != null && countByType > 0) { logger.info(" * Of which " + countByType + " are " + type.toString() + " variants.");
@Override public QueryResult<String> getVariantTypes() { List<String> variantTypes = Arrays.stream(VariantType.values()) .map((value) -> value.name()).collect(Collectors.toList()); QueryResult<String> queryResult = new QueryResult<String>("variant_types", 0, variantTypes.size(), variantTypes.size(), null, null, variantTypes); return queryResult; }
.append(DocumentToVariantConverter.REFERENCE_FIELD, variant.getReference()) .append(DocumentToVariantConverter.ALTERNATE_FIELD, variant.getAlternate()) .append(DocumentToVariantConverter.TYPE_FIELD, variant.getType().name()) .append(DocumentToVariantConverter.IDS_FIELD, variant.getIds()) .append(DocumentToVariantConverter.ANNOTATION_FIELD, Collections.emptyList());
public void setVariantTypeCount(VariantType key, int count) { impl.getVariantTypeCounts().put(key.toString(), count); }
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 ); }
.append(REFERENCE_FIELD, variant.getReference()) .append(ALTERNATE_FIELD, variant.getAlternate()) .append(TYPE_FIELD, variant.getType().name());
public void addVariantTypeCount(VariantType key, int count) { impl.getVariantTypeCounts().put(key.toString(), getVariantTypeCount(key) + count); }