@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); } }