smithlab_cpp/MappedRead.cpp at master · smithlabcode/smithlab_cpp · GitHub

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* Part of SMITHLAB_CPP software

* Andrew D. Smith

* Authors: Andrew D. Smith

* This program is free software: you can redistribute it and/or modify

* it under the terms of the GNU General Public License as published by

* the Free Software Foundation, either version 3 of the License, or

* (at your option) any later version.

* This program is distributed in the hope that it will be useful,

* but WITHOUT ANY WARRANTY; without even the implied warranty of

* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

* GNU General Public License for more details.

* You should have received a copy of the GNU General Public License

* along with this program. If not, see <http://www.gnu.org/licenses/>.

#include "MappedRead.hpp"

#include <algorithm>

#include <cctype>

#include <sstream>

#include <stdexcept>

#include <string>

using std::runtime_error;

using std::string;

MappedRead::MappedRead(const string &line) {

std::istringstream is;

is.rdbuf()->pubsetbuf(const_cast<char *>(line.c_str()), line.size());

string chrom, name, tmp;

size_t start = 0ul, end = 0ul;

char strand = '\0';

double score;

if (is >> chrom >> start >> tmp) {

if (find_if(tmp.begin(), tmp.end(),

[](char c) { return !std::isdigit(c); }) == tmp.end()) {

end = std::stol(tmp);

if (!(is >> name >> score >> strand >> seq))

throw runtime_error("bad line in MappedRead file: " + line);

}

else {

name = tmp;

if (!(is >> score >> strand >> seq))

throw runtime_error("bad line in MappedRead file: " + line);

end = start + seq.length();

}

r = GenomicRegion(chrom, start, end, name, score, strand);

is >> scr;

}

else

throw runtime_error("bad line in MappedRead file: " + line);

}

string MappedRead::tostring() const {

std::ostringstream oss;

oss << r; // no chaining for the << of GenomicRegion

oss << '\t' << seq;

if (!scr.empty())

oss << '\t' << scr;

return oss.str();

}

smithlab_cpp/MappedRead.cpp at master · smithlabcode/smithlab_cpp · GitHub

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