while((option.find_first_of(',') != -1)) { //while there are parameters
m->splitAtComma(value, option);
m->splitAtEquals(key, value);
+ if ((key == "candidate") || (key == "query")) { key = "fasta"; }
+ if (key == "template") { key = "reference"; }
parameters[key] = value;
}
//in case there is no comma and to get last parameter after comma
m->splitAtEquals(key, option);
+ if ((key == "candidate") || (key == "query")) { key = "fasta"; }
+ if (key == "template") { key = "reference"; }
parameters[key] = option;
}
}
if (it->second == "current") {
//look for file types
- if ((it->first == "fasta") || (it->first == "candidate")) {
+ if (it->first == "fasta") {
it->second = m->getFastaFile();
}else if (it->first == "qfile") {
it->second = m->getQualFile();