iterators.add(internalIterator(regions, studyId, sample, gts)); } else { if (operation.equals(QueryOperation.OR)) { throw new IllegalArgumentException("Unable to query by REF or MISS genotypes!"); if (operation.equals(QueryOperation.OR)) { logger.info("Union of " + iterators.size() + " sample indexes"); return new UnionMultiVariantKeyIterator(iterators);
for (Object sampleName : genotypeSamples.keySet()) { if (addOperator) { sb.append(" ").append(queryOperation.name()).append(" ");
if (gtQueryOperation != null && sampleQueryOperation != null && !gtQueryOperation.equals(sampleQueryOperation)) { throw VariantQueryException.incompatibleSampleAndGenotypeOperators();
if (operation == null || operation.equals(QueryOperation.AND)) { sb.append(" AND "); } else { sb.append(' ').append(filtersOperation.name()).append(' '); sb.append(' ').append(qualOperation.name()).append(' '); } else if (fileOperation.equals(QueryOperation.AND)) { sb.append(" AND "); } else { if (genotypeQueryOperation != null && sampleQueryOperation != null && !genotypeQueryOperation.equals(sampleQueryOperation)) { throw VariantQueryException.incompatibleSampleAndGenotypeOperators();
if (isValidParam(query, VariantQueryParam.SAMPLE)) { Pair<QueryOperation, List<String>> pair = splitValue(query.getString(VariantQueryParam.SAMPLE.key())); if (pair.getKey().equals(QueryOperation.AND)) { throw VariantQueryException.malformedParam(VariantQueryParam.SAMPLE, familyId, "Can not be used along with filter \"" + FAMILY.key() + "\" with operator AND (" + AND + ").");
sb.append(infoOperation.toString());
sb.append(formatOperation.toString());
String validatedValue = validatedValues.get(i); if (sb.length() > 0) { sb.append(queryOperation.separator());