From 98decee8c757eb65781630e8760109c6cf294fac Mon Sep 17 00:00:00 2001
From: Rong-Zh <zerelove@icloud.com>
Date: Thu, 20 Feb 2025 14:16:43 +0800
Subject: [PATCH] Escape base quality value as `\"` to avoid json parsing error

---
 src/match.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

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<Match*>& 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;
 }