Method read

DataLayer/FastaReader.cpp:130–421

Read a single record. */

/** Read a single record. */
Sequence FastaReader::read(string& id, string& comment,
		char& anchor, string& q)
{
next_record:
	id.clear();
	comment.clear();
	anchor = 0;
	q.clear();

	// Discard comments.
	while (m_in.peek() == '#')
		ignoreLines(1);

	signed char recordType = m_in.peek();
	Sequence s;

	unsigned qualityOffset = 0;
	if (recordType == EOF || m_in.tellg() >= m_end) {
		m_in.seekg(0, ios::end);
		m_in.clear(std::ios::eofbit | std::ios::failbit);
		return s;
	} else if (recordType == '>' || recordType == '@') {
		// Read the header.
		string header;
		getline(header);
		istringstream headerStream(header);

		// Ignore SAM headers.
		if (header[0] == '@' && isalpha(header[1])
				&& isalpha(header[2]) && header[3] == '\t')
			goto next_record;

		headerStream >> recordType >> id >> ws;
		std::getline(headerStream, comment);

		// Casava FASTQ format
		if (comment.size() > 3
				&& comment[1] == ':' && comment[3] == ':') {
			// read, chastity, flags, index: 1:Y:0:AAAAAA
			if (opt::chastityFilter && comment[2] == 'Y') {
				m_unchaste++;
				if (recordType == '@') {
					ignoreLines(3);
				} else {
					while (m_in.peek() != '>' && m_in.peek() != '#'
							&& ignoreLines(1))
						;
				}
				goto next_record;
			}
			if (id.size() > 2 && id.rbegin()[1] != '/') {
				// Add the read number to the ID.
				id += '/';
				id += comment[0];
			}
		}

		getline(s);