Esempio n. 1
0
int read_sequences(Auto_Unzip & input, int num_seq, Mask sequences[], Fasta::FASTQ_encoding format_type, bool gui_output) {
	if (&input == NULL)
		return 0;

	Fasta read;
	read.set_FASTQ_type(format_type);
	int n_seq = 0;
	{
		mutex::scoped_lock lock(read_mutex);
		istream & in = input.filtered();
		while (not input.eof() and n_seq < num_seq) {
			in >> read;
			if (read.length() > MAX_READ_LENGTH) {
				cerr << "Read " << read.get_id() << " too long. Max allowed read size is " << MAX_READ_LENGTH << endl;
				exit(5);
			}
			//Reset and take a ref
			Mask & r = sequences[n_seq] = Mask();
			r.set_id(read.get_id());
			r.set_sequence(read.get_sequence());
			r.set_quality(read.get_quality());
			n_seq++;
		}
		output_progress(input, gui_output);
	}
	return n_seq;
}
Esempio n. 2
0
int read_sequences(Auto_Unzip & first, Auto_Unzip & second, int num_seq, Mask sequences[], Fasta::FASTQ_encoding format_type, bool gui_output) {
	if (&first == NULL or &second == NULL)
		return 0;

	Fasta read;
	read.set_FASTQ_type(format_type);
	int n_seq = 0;
	{
		mutex::scoped_lock lock(read_mutex);
		istream & first_in = first.filtered();
		istream & second_in = second.filtered();
		while (not first.eof() and not second.eof() and (n_seq + 1) < num_seq) {
			first_in >> read;
			if (read.length() > MAX_READ_LENGTH) {
				cerr << "Read " << read.get_id() << " too long. Max allowed read size is " << MAX_READ_LENGTH << endl;
				exit(5);
			}
			Mask & rf = sequences[n_seq];
			rf.set_id(read.get_id());
			rf.set_sequence(read.get_sequence());
			rf.set_quality(read.get_quality());
			n_seq++;
			second_in >> read;
			if (read.length() > MAX_READ_LENGTH) {
				cerr << "Read " << read.get_id() << " too long. Max allowed read size is " << MAX_READ_LENGTH << endl;
				exit(5);
			}
			Mask & rs = sequences[n_seq];
			rs.set_id(read.get_id());
			rs.set_sequence(read.get_sequence());
			rs.set_quality(read.get_quality());
			n_seq++;
			//CHECK!!
			if (rf.id.compare(0, rf.id.size() - 1, rs.id, 0, rs.id.size() - 1) != 0) {
				ERROR_CHANNEL << "wrong paired reads IDs: '" << rf.id << "' and '" << rs.id << '\'' << endl;
				exit(2);
			}
		}
		output_progress(first, gui_output);
	}
	return n_seq;
}