for(int i=0;i<fastaFileNames.size();i++){
if (isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
+ else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
else {
ifstream inFASTA;
string seqName;
int success = 1;
Sequence currSeq(inFASTA);
- cout << i << '\t' << currSeq.getName() << endl;
+
string origSeq = currSeq.getUnaligned();
if (origSeq != "") {
int groupBar, groupPrime;
}
}
outGroups << currSeq.getName() << '\t' << thisGroup << endl;
-
if(allFiles){
currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
}
groupVector.push_back(group);
if(allFiles){
- if (group != "") { //there is a group for this primer
+ outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
+ if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
+ filesToRemove.insert((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
+ }else {
outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
- outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
}
}