public int getVariantTypeCount(VariantType key) { return impl.getVariantTypeCounts().getOrDefault(key.toString(), 0); }
public void setVariantTypeCount(VariantType key, int count) { impl.getVariantTypeCounts().put(key.toString(), count); }
public void addVariantTypeCount(VariantType key, int count) { impl.getVariantTypeCounts().put(key.toString(), getVariantTypeCount(key) + count); }
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 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()); } } } }
private void createTypeQuery(Query query, String typeQueryParam, String svTypeQueryParam, String typeMongoField, String svTypeMongoField, List<Bson> andBsonList) { if (query != null && StringUtils.isNotBlank(query.getString(typeQueryParam))) { List<Bson> orBsonList = new ArrayList<>(); String variantTypeString = query.getString(typeQueryParam); if (variantTypeString.equals(VariantType.DELETION.toString()) || (StructuralVariantType.COPY_NUMBER_LOSS.toString().equals(query.getString(svTypeQueryParam)))) { orBsonList.add(Filters.eq(typeMongoField, VariantType.DELETION.toString())); orBsonList.add(Filters.eq(svTypeMongoField, StructuralVariantType.COPY_NUMBER_LOSS.toString())); andBsonList.add(Filters.or(orBsonList)); } else if (variantTypeString.equals(VariantType.INSERTION.toString()) || variantTypeString.equals(VariantType.DUPLICATION.toString()) || StructuralVariantType.COPY_NUMBER_GAIN.toString().equals(query.getString(svTypeQueryParam))) { orBsonList.add(Filters.eq(typeMongoField, VariantType.INSERTION.toString())); orBsonList.add(Filters.eq(typeMongoField, VariantType.DUPLICATION.toString())); orBsonList.add(Filters.eq(svTypeMongoField, StructuralVariantType.COPY_NUMBER_GAIN.toString())); andBsonList.add(Filters.or(orBsonList)); // Inversion or just CNV (without subtype) } else { andBsonList.add(Filters.eq(typeMongoField, variantTypeString.toString())); } } }
private void createTypeQuery(Query query, String typeQueryParam, String svTypeQueryParam, String typeMongoField, String svTypeMongoField, List<Bson> andBsonList) { if (query != null && StringUtils.isNotBlank(query.getString(typeQueryParam))) { List<Bson> orBsonList = new ArrayList<>(); String variantTypeString = query.getString(typeQueryParam); if (variantTypeString.equals(VariantType.DELETION.toString()) || (StructuralVariantType.COPY_NUMBER_LOSS.toString().equals(query.getString(svTypeQueryParam)))) { orBsonList.add(Filters.eq(typeMongoField, VariantType.DELETION.toString())); orBsonList.add(Filters.eq(svTypeMongoField, StructuralVariantType.COPY_NUMBER_LOSS.toString())); andBsonList.add(Filters.or(orBsonList)); } else if (variantTypeString.equals(VariantType.INSERTION.toString()) || variantTypeString.equals(VariantType.DUPLICATION.toString()) || StructuralVariantType.COPY_NUMBER_GAIN.toString().equals(query.getString(svTypeQueryParam))) { orBsonList.add(Filters.eq(typeMongoField, VariantType.INSERTION.toString())); orBsonList.add(Filters.eq(typeMongoField, VariantType.DUPLICATION.toString())); orBsonList.add(Filters.eq(svTypeMongoField, StructuralVariantType.COPY_NUMBER_GAIN.toString())); andBsonList.add(Filters.or(orBsonList)); // Inversion or just CNV (without subtype) } else { andBsonList.add(Filters.eq(typeMongoField, variantTypeString.toString())); } } }
alt.put(ALTERNATES_START, coordinate.getStart() != null ? coordinate.getStart() : variant.getStart()); alt.put(ALTERNATES_END, coordinate.getEnd() != null ? coordinate.getEnd() : variant.getEnd()); alt.put(ALTERNATES_TYPE, coordinate.getType() != null ? coordinate.getType().toString() : variant.getType().toString()); alternates.add(alt);
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.");
variantSearchModel.setStart(variant.getStart()); variantSearchModel.setEnd(variant.getEnd()); variantSearchModel.setType(variant.getType().toString());
map.put(TYPE, variantType.toString());
@Test public void queryArchiveTable() { final int[] numVariants = {0}; Map<String, Integer> variantCounts = new HashMap<>(); System.out.println("Query from Archive table"); dbAdaptor.iterator( new Query() .append(VariantQueryParam.STUDY.key(), studyConfiguration.getStudyId()) .append(VariantQueryParam.FILE.key(), FILE_ID), new QueryOptions("archive", true)).forEachRemaining(variant -> { System.out.println("Variant from archive = " + variant.toJson()); numVariants[0]++; variantCounts.compute(variant.getType().toString(), (s, integer) -> integer == null ? 1 : (integer + 1)); }); System.out.println("End query from Archive table"); fileMetadata.getStats().getVariantTypeCounts().forEach((s, integer) -> assertEquals(integer, variantCounts.getOrDefault(s, 0))); assertEquals(fileMetadata.getStats().getNumVariants(), numVariants[0]); }
List<String> types = new ArrayList<>(subTypes.size() + 1); types.add(s); subTypes.forEach(subType -> types.add(subType.toString())); return types;
byte[] rowKey = VariantPhoenixKeyFactory.generateVariantRowKey(variant); Put put = new Put(rowKey); add(put, VariantPhoenixHelper.VariantColumn.TYPE, variant.getType().toString()); if (variant.getSv() != null) { if (variant.getSv().getCiStartLeft() != null) {
query.append(QueryParams.SV_TYPE.key(), variant.getSv().getType().toString()); query.append(QueryParams.TYPE.key(), variant.getType().toString());
query.append(QueryParams.SV_TYPE.key(), variant.getSv().getType().toString()); query.append(QueryParams.TYPE.key(), variant.getType().toString());