int main(void) {
// Test the fastareader
string filename = "/home/laozzzzz/barcode_project/reads/e_coli_10000snp.fa";
bool done = false;
bool success = false;
Sequence read;
std::unique_ptr<SequenceReader> reader(FastaReader::CreateSequenceReader(filename));
while(!success) {
reader->NextRead(read, success, done);
cout<< read.fowardSeq() <<endl;
}
read.clear();
filename = "/home/laozzzzz/barcode_project/reads/1000.fq";
done = false;
success = false;
reader.reset(FastqReader::CreateSequenceReader(filename));
while(!success) {
reader->NextRead(read, success, done);
cout<< read.fowardSeq() <<endl;
}
return 0;
}
void FastaReader::NextRead(Sequence &r, bool &success, bool &done) {
if (!r.empty())
r.clear();
int c;
success = false;
done = false;
// Pick off the first at
if(this->first_) {
c = fHandler_->get();
if(c != '>') {
c = fHandler_->getPastNewline();
if(c < 0) {
r.clear();success = false; done = true;
}
}
if(c != '>') {
std::cerr << "Error: reads file does not look like a FASTA file" << std::endl;
throw 1;
}
assert_eq('>', c);
first_ = false;
}
// Read to the end of the id line, sticking everything after the '>'
// into *name
string& id = r.id();
while(true) {
c = fHandler_->get();
if(c < 0) {
r.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTA file" << std::endl;
throw 1;
}
if(c == '\n' || c == '\r') {
// Break at end of line, after consuming all \r's, \n's
while(c == '\n' || c == '\r') {
c = fHandler_->get();
if(c < 0) {
r.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTA file" << std::endl;
throw 1;
}
}
break;
}
if(c == '>')
continue;
id += c;
//name.append(c);
}
// fb_ now points just past the first character of a
// sequence line, and c holds the first character
BTDnaString& sbuf = r.fowardSeq();
while(true){
c = toupper(c);
if(c < 0){
r.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTA file" << std::endl;
throw 1;
}
else{
if(c == '\n' || c == '\r') {
break;
}
sbuf.append(asc2dna[c]);
c = fHandler_->get();
}
}
success = true;
done = fHandler_->eof();
is_done_ = done;
}
void fastqPattern::parseImp(Sequence& read,
bool& success,
bool& done){
char c;
success = false;
done = false;
// Pick off the first at
if(this->first_) {
c = this->fb_->get();
if(c != '@') {
c = this->fb_->getPastNewline();
if(c < 0) {
success = false; done = true;
}
line_num_ += 1;
}
if(c != '@') {
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
assert_eq('@', c);
first_ = false;
}
// Read to the end of the id line, sticking everything after the '@'
// into id
std::string& id = read.id();
while(true) {
c = this->fb_->get();
if(c == '@')
continue;
if(c < 0) {
read.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
if(c == '\n' || c == '\r') {
// Break at end of line, after consuming all \r's, \n's
while(c == '\n' || c == '\r') {
c = this->fb_->get();
if(c < 0) {
read.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
}
line_num_ += 1;
break;
}
id += c;
}
// fb_ now points just past the first character of a
// sequence line, and c holds the first character
//BTDnaString& sbuf = r->fowardSeq();
std::string& sequence = read.fowardSeq();
while(true){
c = toupper(c);
if(c < 0){
read.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
else{
if(c == '\n' || c == '\r') {
// Break at end of line, after consuming all \r's, \n's
while(c == '\n' || c == '\r') {
c = this->fb_->get();
if(c < 0) {
read.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
}
line_num_ += 1;
break;
}
// convert N to A
if(toupper(c) == 'N')
c = 'A';
sequence += c;
c = this->fb_->get();
}
}
assert_eq('+', c);
// skip the option sequence at '+' line
c = this->fb_->getPastNewline();
line_num_ += 1;
if(c <0){
read.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
string& qual = read.quality();
while(true){
qual += c;
c = this->fb_->get();
if(c == '\n' || c == '\r')
break;
}
line_num_ += 1;
success = true;
assert(qual.length() == sequence.length());
done = fb_->eof();
}
