Escape quality string characters in JSON output

[a113n]

Escape special characters properly in the jsonreporter.cpp output.

[Copilot]

Pull request overview

This PR ensures generated JSON reports remain valid by escaping special characters in string fields written by the JSON reporter and read serialization helpers.

Changes:

• Added escapeJsonString(const std::string&) utility in common.* to JSON-escape strings.
• Updated JsonReporter::run() to escape command/time and various fusion string fields before writing JSON.
• Updated Match::printReadToJson() to escape read sequence and quality strings before writing JSON.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
src/match.cpp	Escapes read seq and qual fields before writing JSON.
src/jsonreporter.cpp	Escapes command/time and fusion-related string fields (including object keys) in JSON output.
src/common.h	Declares escapeJsonString and includes <string> for the declaration.
src/common.cpp	Implements JSON string escaping helper.

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[Copilot]

escapeJsonString is formatted with tab indentation, while most of the codebase uses spaces (e.g., other .cpp files in src/). Please reformat this function to avoid mixed whitespace and keep style consistent.

Suggested change

	std::string output;
	output.reserve(input.size());
	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;
	}
	}
	return output;
	std::string output;
	output.reserve(input.size());
	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;
	}
	}
	return output;

[Copilot]

escapeJsonString(...) allocates a new std::string for every call. Since JsonReporter::run() calls it inside nested loops (per fusion and then per read via printReadToJson), this can add overhead for large JSON reports. Consider adding a helper that writes escaped content directly to the stream (or reuses a buffer) to avoid repeated allocations/copies.