Function readContigs

Consensus/Consensus.cpp:107–148

Read all contigs in and store the contigs in g_contigs and make a * g_baseCounts, to store pile-up for each base. */

/** Read all contigs in and store the contigs in g_contigs and make a
 * g_baseCounts, to store pile-up for each base. */
static void readContigs(const string& contigsPath)
{
	FastaReader contigsFile(contigsPath.c_str(),
			FastaReader::NO_FOLD_CASE);
	int count = 0;
	for (FastaRecord rec; contigsFile >> rec;) {
		const Sequence& seq = rec.seq;
		ContigCount& contig = g_contigs[rec.id];
		contig.seq = seq;

		istringstream ss(rec.comment);
		unsigned length;
		contig.coverage = 0;
		ss >> length >> contig.coverage >> ws;
		getline(ss, contig.comment);

		if (count == 0) {
			// Detect colour-space contigs.
			opt::colourSpace = isdigit(seq[0]);
			if (!opt::outputCS)
				opt::csToNt = opt::colourSpace;
			else if (!opt::colourSpace) {
				cerr << "error: Cannot convert nucleotide data to "
					"colour space.\n";
				exit(EXIT_FAILURE);
			}
		} else {
			if (opt::colourSpace)
				assert(isdigit(seq[0]));
			else
				assert(isalpha(seq[0]));
		}

		contig.counts = BaseCounts(contig.seq.length()
				+ (opt::csToNt ? 1 : 0));

		count++;
	}
	cerr << "Read " << count << " contigs\n";
	assert(contigsFile.eof());
	assert(count > 0);
}

typedef vector<Alignment> AlignmentVector;