diff --git a/src/match.cpp b/src/match.cpp index 1f81a6d..abf4218 100644 --- a/src/match.cpp +++ b/src/match.cpp @@ -88,7 +88,8 @@ int Match::countUnique(vector& matches) { return count; } +// Escape base quality value as `\"` to avoid json parsing error void Match::printReadToJson(ofstream& file, string pad) { file << pad << "\"seq\":" << "\"" << mRead->mSeq.mStr << "\"," << endl; - file << pad << "\"qual\":" << "\"" << mRead->mQuality << "\"" << endl; + file << pad << "\"qual\":" << "\"" << replace(mRead->mQuality, "\"", "\\\"") << "\"" << endl; }