FastqRead::FastqRead(Sequence s, QualityScores q, string f) {
try {
m = MothurOut::getInstance(); format = f;
//fill convert table - goes from solexa to sanger. Used fq_all2std.pl as a reference.
for (int i = -64; i < 65; i++) {
char temp = (char) ((int)(33 + 10*log(1+pow(10,(i/10.0)))/log(10)+0.499));
convertTable.push_back(temp);
convertBackTable.push_back(((int)(33 + 10*log(1+pow(10,(i/10.0)))/log(10)+0.499)));
}
if (s.getName() != q.getName()) { m->mothurOut("[ERROR]: sequence name does not match quality score name. Cannot construct fastq object.\n"); m->control_pressed = true; }
else {
name = s.getName();
comment = s.getComment();
sequence = s.getUnaligned();
scores = q.getScores();
scoreString = convertQual(scores);
}
}
catch(exception& e) {
m->errorOut(e, "FastqRead", "FastqRead");
exit(1);
}
}
struct Functor { void operator () (Sequence& s) const
{
// We dump the data size and the comment
std::cout << "[" << s.getDataSize() << "] " << s.getComment() << std::endl;
// We dump the data
std::cout << s.toString () << std::endl;
}};
