Function buildBaseQuality

Consensus/Consensus.cpp:174–268

Builds the pile up of all reads based on the alignments and * read sequence */

/** Builds the pile up of all reads based on the alignments and
 * read sequence */
static void buildBaseQuality()
{
	if (opt::csToNt)
		opt::colourSpace = false;

	// for each read and/or set of alignments.
	for (string line; getline(cin, line);) {
		string readID;
		Sequence seq;
		AlignmentVector alignments;

		readAlignment(line, readID, seq, alignments);

		// If converting to NT space, check that at least one of the
		// alignments starts at read location 0. Otherwise, it is
		// likely to introduce a frameshift or erroneous sequence in
		// the final consensus.
		if (opt::csToNt) {
			bool good = false;
			for (AlignmentVector::const_iterator
					alignIter = alignments.begin();
					alignIter != alignments.end(); ++alignIter) {
				if (alignIter->read_start_pos == 0) {
					good = true;
					break;
				}
			}
			if (!good)
				continue;
		}

		// For each alignment for the read.
		for (AlignmentVector::const_iterator
				alignIter = alignments.begin();
				alignIter != alignments.end(); ++alignIter) {
			string seqrc;
			Alignment a;
			if (alignIter->isRC) {
				seqrc = reverseComplement(seq);
				a = alignIter->flipQuery();
			} else {
				seqrc = seq;
				a = *alignIter;
			}
			const char* s = seqrc.c_str();

			ContigMap::iterator contigIt = g_contigs.find(a.contig);
			if (contigIt == g_contigs.end()) {
				cerr << "error: unexpected contig ID: `" << a.contig
					<< "'\n";
				exit(EXIT_FAILURE);
			}

			BaseCounts& countsVec = contigIt->second.counts;

			int read_min;
			int read_max;
			if (!opt::csToNt) {