Submitter: phoebe.xin.leung Email: pho

some problems met when configure meerkat-src-bre about software-issues HOT 1 OPEN

parklab commented on July 30, 2024

some problems met when configure meerkat-src-bre

from software-issues.

Comments (1)

vflorelo commented on July 30, 2024

I am no expert in C++ but this fixed my installation

Original code:

		if (line.find("Median insert size") != string::npos) {
			rg = get_rg(line);
			getline(isf, line);
			double val = strtod(line.c_str(), NULL);
			map< string, pair<double,double> >::iterator iter =
				isinfo.find(rg);
			if (iter != isinfo.end())
				isinfo[rg].first = val;
			else
				isinfo[rg] = make_pair<double,double>(val, 0);
		} else if (line.find("Standard deviation of insert size") != string::npos) {
			rg = get_rg(line);
			getline(isf, line);
			double val = strtod(line.c_str(), NULL);
			map< string, pair<double,double> >::iterator iter =
				isinfo.find(rg);
			if (iter != isinfo.end())
				isinfo[rg].second = val;
			else
				isinfo[rg] = make_pair<double,double>(0, val);
		}

Patch:

		if (line.find("Median insert size") != string::npos) {
			rg = get_rg(line);
			getline(isf, line);
			double val = strtod(line.c_str(), NULL);
			map< string, pair<double,double> >::iterator iter =
				isinfo.find(rg);
			if (iter != isinfo.end())
				isinfo[rg].first = val;
			else
				isinfo[rg] = make_pair<double&,double>(val, 0);
		} else if (line.find("Standard deviation of insert size") != string::npos) {
			rg = get_rg(line);
			getline(isf, line);
			double val = strtod(line.c_str(), NULL);
			map< string, pair<double,double> >::iterator iter =
				isinfo.find(rg);
			if (iter != isinfo.end())
				isinfo[rg].second = val;
			else
				isinfo[rg] = make_pair<double,double&>(0, val);
		}

Nothe the ampersand in the function call make_pair

From stack overflow:
https://stackoverflow.com/questions/7388889/whats-a-variable-with-double

It's a reference. That means that whatever you set the value to inside the function, the original variable that was passed in from outside will have that value.

But in the function make_pair, the variable val was not being called by reference

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