}
m->gobble(in);
+ if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ", forward = " + forward + ", reverse = " + reverse + ".\n"); }
//check to make sure both are able to be opened
ifstream in2;
}
//roligo = reverseOligo(roligo);
+ if (m->debug) { m->mothurOut("[DEBUG]: reading - " + roligo + ".\n"); }
+
group = "";
// get rest of line in case there is a primer name
while (!in.eof()) {
char c = in.get();
- if (c == 10 || c == 13){ break; }
+ if (c == 10 || c == 13 || c == -1){ break; }
else if (c == 32 || c == 9){;} //space or tab
else { group += c; }
}
oligosPair newPrimer(foligo, roligo);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
//check for repeat barcodes
string tempPair = foligo+roligo;
group = "";
while (!in.eof()) {
char c = in.get();
- if (c == 10 || c == 13){ break; }
+ if (c == 10 || c == 13 || c == -1){ break; }
else if (c == 32 || c == 9){;} //space or tab
else { group += c; }
}