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;
}
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;
}