Function readAlignment

ParseAligns/ParseAligns.cpp:412–441

}

static void
readAlignment(const string& line, ReadAlignMap& out)
{
	istringstream s(line);
	pair<string, AlignmentVector> v;
	switch (opt::inputFormat) {
	case opt::SAM: {
		SAMRecord sam;
		s >> sam;
		assert(s);
		v.first = sam.qname;
		if (sam.isRead1())
			v.first += "/1";
		else if (sam.isRead2())
			v.first += "/2";
		if (!sam.isUnmapped())
			v.second.push_back(sam);
		break;
	}
	case opt::KALIGNER: {
		s >> v.first;
		assert(s);
		v.second.reserve(count(line.begin(), line.end(), '\t'));
		v.second.assign(istream_iterator<Alignment>(s), istream_iterator<Alignment>());
		assert(s.eof());
		break;
	}
	}
	handleAlignment(v, out);
}

static void
readAlignments(istream& in, ReadAlignMap* pout)