Function handleAlignmentPair

ParseAligns/ParseAligns.cpp:308–366

}

static void
handleAlignmentPair(const ReadAlignMap::value_type& curr, const ReadAlignMap::value_type& pair)
{
	const string& currID = curr.first;
	const string& pairID = pair.first;

	// Both reads must align to a unique location.
	// The reads are allowed to span more than one contig, but
	// at least one of the two reads must span no more than
	// two contigs.
	const unsigned MAX_SPAN = 2;
	if (curr.second.empty() && pair.second.empty()) {
		stats.bothUnaligned++;
	} else if (curr.second.empty() || pair.second.empty()) {
		stats.oneUnaligned++;
	} else if (!checkUniqueAlignments(curr.second) || !checkUniqueAlignments(pair.second)) {
		stats.numMulti++;
	} else if (curr.second.size() > MAX_SPAN && pair.second.size() > MAX_SPAN) {
		stats.numSplit++;
	} else {
		// Iterate over the vectors, outputting the aligments
		bool counted = false;
		for (AlignmentVector::const_iterator refAlignIter = curr.second.begin();
		     refAlignIter != curr.second.end();
		     ++refAlignIter) {
			for (AlignmentVector::const_iterator pairAlignIter = pair.second.begin();
			     pairAlignIter != pair.second.end();
			     ++pairAlignIter) {
				const Alignment& a0 = flipAlignment(*refAlignIter, currID);
				const Alignment& a1 = flipAlignment(*pairAlignIter, pairID);

				bool sameTarget = a0.contig == a1.contig;
				if (sameTarget && curr.second.size() == 1 && pair.second.size() == 1) {
					// Same target and the only alignment.
					if (a0.isRC != a1.isRC) {
						// Correctly oriented. Add this alignment to
						// the distribution of fragment sizes.
						int size = fragmentSize(a0, a1);
						histogram.insert(size);
						if (!opt::fragPath.empty()) {
							fragFile << size << '\n';
							assert(fragFile.good());
						}
					} else
						stats.numFF++;
					counted = true;
				}

				bool outputSameTarget = opt::fragPath.empty() && opt::histPath.empty();
				if (!sameTarget || outputSameTarget) {
					cout << SAMRecord(a0, a1) << '\n' << SAMRecord(a1, a0) << '\n';
					assert(cout.good());
				}
			}
		}
		if (!counted)
			stats.numDifferent++;
	}