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Escape quality string characters in JSON output #49

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0508f19
Escape quality string characters in JSON output
a113n Apr 24, 2026
df7dc0f
Fix JSON escaping and stream escaped output
a113n Apr 24, 2026
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41 changes: 40 additions & 1 deletion src/common.cpp
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Original file line number Diff line number Diff line change
@@ -1 +1,40 @@
#include "common.h"
#include "common.h"

void writeEscapedJsonString(std::ostream& output, const std::string& input) {
for(size_t i = 0; i < input.size(); i++) {
const unsigned char c = static_cast<unsigned char>(input[i]);
switch(c) {
case '"':
output << "\\\"";
break;
case '\\':
output << "\\\\";
break;
case '\b':
output << "\\b";
break;
case '\f':
output << "\\f";
break;
case '\n':
output << "\\n";
break;
case '\r':
output << "\\r";
break;
case '\t':
output << "\\t";
break;
default:
if(c < 0x20) {
const char* hex = "0123456789abcdef";
output << "\\u00";
output << hex[(c >> 4) & 0x0F];
output << hex[c & 0x0F];
} else {
output << static_cast<char>(c);
}
break;
}
}
}
4 changes: 4 additions & 0 deletions src/common.h
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Original file line number Diff line number Diff line change
@@ -1,6 +1,9 @@
#ifndef COMMON_H
#define COMMON_H

#include <ostream>
#include <string>

#define FUSIONSCAN_VER "0.8.0"

#define _DEBUG true
Expand Down Expand Up @@ -42,5 +45,6 @@ static const int PACK_IN_MEM_LIMIT = 100;
static const int DUPE_NORMAL_LEVEL = -1;
static const int DUPE_HIGH_LEVEL = -2;

void writeEscapedJsonString(std::ostream& output, const std::string& input);

#endif /* COMMON_H */
52 changes: 39 additions & 13 deletions src/jsonreporter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,13 @@ extern string command;

void JsonReporter::run() {
mFile << "{" << endl;
mFile << "\t\"command\":\"" << command << "\"," << endl;
mFile << "\t\"command\":\"";
writeEscapedJsonString(mFile, command);
mFile << "\"," << endl;
mFile << "\t\"version\":\"" << FUSIONSCAN_VER << "\"," << endl;
mFile << "\t\"time\":\"" << getCurrentSystemTime() << "\"," << endl;
mFile << "\t\"time\":\"";
writeEscapedJsonString(mFile, getCurrentSystemTime());
mFile << "\"," << endl;
mFile << "\t\"fusions\":{";

bool isFirstMut = true;
Expand All @@ -42,25 +46,47 @@ void JsonReporter::run() {
else
mFile << "," << endl;

mFile << "\t\t\"" << fusion.mTitle << "\":{" << endl;
mFile << "\t\t\"";
writeEscapedJsonString(mFile, fusion.mTitle);
mFile << "\":{" << endl;
mFile << "\t\t\t\"" << "left" << "\":{" << endl;
mFile << "\t\t\t\t\"" << "gene_name" << "\":" << "\"" << fusion.mLeftGene.mName << "\"," << endl;
mFile << "\t\t\t\t\"" << "gene_chr" << "\":" << "\"" << fusion.mLeftGene.mChr << "\"," << endl;
mFile << "\t\t\t\t\"" << "gene_name" << "\":\"";
writeEscapedJsonString(mFile, fusion.mLeftGene.mName);
mFile << "\"," << endl;
mFile << "\t\t\t\t\"" << "gene_chr" << "\":\"";
writeEscapedJsonString(mFile, fusion.mLeftGene.mChr);
mFile << "\"," << endl;
mFile << "\t\t\t\t\"" << "position" << "\":" << fusion.mLeftGene.genePos2ChrPos(fusion.mLeftGP.position) << "," << endl;
mFile << "\t\t\t\t\"" << "reference" << "\":" << "\"" << fusion.mLeftRef << "\"," << endl;
mFile << "\t\t\t\t\"" << "ref_ext" << "\":" << "\"" << fusion.mLeftRefExt << "\"," << endl;
mFile << "\t\t\t\t\"" << "pos_str" << "\":" << "\"" << fusion.mLeftPos << "\"," << endl;
mFile << "\t\t\t\t\"" << "reference" << "\":\"";
writeEscapedJsonString(mFile, fusion.mLeftRef);
mFile << "\"," << endl;
mFile << "\t\t\t\t\"" << "ref_ext" << "\":\"";
writeEscapedJsonString(mFile, fusion.mLeftRefExt);
mFile << "\"," << endl;
mFile << "\t\t\t\t\"" << "pos_str" << "\":\"";
writeEscapedJsonString(mFile, fusion.mLeftPos);
mFile << "\"," << endl;
mFile << "\t\t\t\t\"" << "exon_or_intron" << "\":" << "\"" << (fusion.mLeftIsExon?"exon":"intron") << "\"," << endl;
mFile << "\t\t\t\t\"" << "exon_or_intron_id" << "\":" << fusion.mLeftExonOrIntronID << "," << endl;
mFile << "\t\t\t\t\"" << "strand" << "\":" << "\"" << (fusion.isLeftProteinForward()?"forward":"reversed") << "\"" << endl;
mFile << "\t\t\t}, " << endl;
mFile << "\t\t\t\"" << "right" << "\":{" << endl;
mFile << "\t\t\t\t\"" << "gene_name" << "\":" << "\"" << fusion.mRightGene.mName << "\"," << endl;
mFile << "\t\t\t\t\"" << "gene_chr" << "\":" << "\"" << fusion.mRightGene.mChr << "\"," << endl;
mFile << "\t\t\t\t\"" << "gene_name" << "\":\"";
writeEscapedJsonString(mFile, fusion.mRightGene.mName);
mFile << "\"," << endl;
mFile << "\t\t\t\t\"" << "gene_chr" << "\":\"";
writeEscapedJsonString(mFile, fusion.mRightGene.mChr);
mFile << "\"," << endl;
mFile << "\t\t\t\t\"" << "position" << "\":" << fusion.mRightGene.genePos2ChrPos(fusion.mRightGP.position) << "," << endl;
mFile << "\t\t\t\t\"" << "reference" << "\":" << "\"" << fusion.mRightRef << "\"," << endl;
mFile << "\t\t\t\t\"" << "ref_ext" << "\":" << "\"" << fusion.mRightRefExt << "\"," << endl;
mFile << "\t\t\t\t\"" << "pos_str" << "\":" << "\"" << fusion.mRightPos << "\"," << endl;
mFile << "\t\t\t\t\"" << "reference" << "\":\"";
writeEscapedJsonString(mFile, fusion.mRightRef);
mFile << "\"," << endl;
mFile << "\t\t\t\t\"" << "ref_ext" << "\":\"";
writeEscapedJsonString(mFile, fusion.mRightRefExt);
mFile << "\"," << endl;
mFile << "\t\t\t\t\"" << "pos_str" << "\":\"";
writeEscapedJsonString(mFile, fusion.mRightPos);
mFile << "\"," << endl;
mFile << "\t\t\t\t\"" << "exon_or_intron" << "\":" << "\"" << (fusion.mRightIsExon?"exon":"intron") << "\"," << endl;
mFile << "\t\t\t\t\"" << "exon_or_intron_id" << "\":" << fusion.mRightExonOrIntronID << "," << endl;
mFile << "\t\t\t\t\"" << "strand" << "\":" << "\"" << (fusion.isRightProteinForward()?"forward":"reversed") << "\"" << endl;
Expand Down
8 changes: 6 additions & 2 deletions src/match.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -89,6 +89,10 @@ int Match::countUnique(vector<Match*>& matches) {
}

void Match::printReadToJson(ofstream& file, string pad) {
file << pad << "\"seq\":" << "\"" << mRead->mSeq.mStr << "\"," << endl;
file << pad << "\"qual\":" << "\"" << mRead->mQuality << "\"" << endl;
file << pad << "\"seq\":\"";
writeEscapedJsonString(file, mRead->mSeq.mStr);
file << "\"," << endl;
file << pad << "\"qual\":\"";
writeEscapedJsonString(file, mRead->mQuality);
file << "\"" << endl;
}