int success = 1;
Sequence currSeq(inFASTA);
-
+ cout << i << '\t' << currSeq.getName() << endl;
string origSeq = currSeq.getUnaligned();
if (origSeq != "") {
int groupBar, groupPrime;
while(!inOligos.eof()){
inOligos >> type;
-
+
if(type[0] == '#'){
while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
}
else{
+ //make type case insensitive
+ for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
+
inOligos >> oligo;
for(int i=0;i<oligo.length();i++){
if(oligo[i] == 'U') { oligo[i] = 'T'; }
}
- if(type == "forward"){
+ if(type == "FORWARD"){
group = "";
// get rest of line in case there is a primer name
outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
}
}
+
}
- else if(type == "reverse"){
+ else if(type == "REVERSE"){
Sequence oligoRC("reverse", oligo);
oligoRC.reverseComplement();
revPrimer.push_back(oligoRC.getUnaligned());
}
- else if(type == "barcode"){
+ else if(type == "BARCODE"){
inOligos >> group;
//check for repeat barcodes