Function writeEstimates

DistanceEst/DistanceEst.cpp:338–377

Generate distance estimates for the specified alignments. */

/** Generate distance estimates for the specified alignments. */
static void writeEstimates(ostream& out,
		const vector<SAMRecord>& pairs,
		const vector<unsigned>& lengthVec, const PMF& pmf)
{
	assert(!pairs.empty());
	ContigID id0(get(g_contigNames, pairs.front().rname));
	assert(id0 < lengthVec.size());
	unsigned len0 = lengthVec[id0];
	if (len0 < opt::seedLen)
		return; // Skip contigs shorter than the seed length.

	ostringstream ss;
	if (opt::format == DIST)
		ss << pairs.front().rname;

	typedef map<ContigNode, Pairs> PairsMap;
	PairsMap dataMap[2];
	for (Pairs::const_iterator it = pairs.begin();
			it != pairs.end(); ++it)
		dataMap[it->isReverse()][find_vertex(
				it->mrnm, it->isReverse() == it->isMateReverse(),
				g_contigNames)]
			.push_back(*it);

	for (int sense0 = false; sense0 <= true; sense0++) {
		if (opt::format == DIST && sense0)
			ss << " ;";
		const PairsMap& x = dataMap[sense0 ^ opt::rf];
		for (PairsMap::const_iterator it = x.begin();
				it != x.end(); ++it)
			writeEstimate(opt::format == DIST ? ss : out,
					ContigNode(id0, sense0), it->first,
					len0, lengthVec[it->first.id()],
					it->second, pmf);
	}
	if (opt::format == DIST)
#pragma omp critical(out)
		out << ss.str() << '\n';
	assert(out.good());
}

/** Load a histogram from the specified file. */
static Histogram loadHist(const string& path)