@Override
public String queryVariantRaw(
ExtendedFileInfo file, String chromosome, VariantFetchParams params) {
params.setFormat(ReturnFormat.vcf);
String rtn = queryVariantsInternal(file, chromosome, params);
logger.info(rtn);
return rtn;
}
@Override
public List<VariantRecord> queryVariantJSON(
ExtendedFileInfo file, String chromosome, VariantFetchParams params) {
try {
params.setFormat(ReturnFormat.json);
String rtn = queryVariantsInternal(file, chromosome, params);
logger.info(rtn);
JsonNode responseNode = mapper.readValue(rtn, JsonNode.class).findPath(ITEMS);
List<VariantRecord> records = new ArrayList<VariantRecord>();
for (int i = 0; i < responseNode.size(); i++) {
records.add(
(VariantRecord) mapper.readValue(responseNode.get(i).toString(), VariantRecord.class));
}
return records;
} catch (BaseSpaceException bs) {
throw bs;
} catch (Throwable t) {
throw new RuntimeException("Error during JSON query " + t);
}
}