//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
fastaFileName = validParameter.validFile(parameters, "fasta", true);
if (fastaFileName == "not open") { abort = true; }
else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else { m->setFastaFile(fastaFileName); }
qualFileName = validParameter.validFile(parameters, "qfile", true);
if (qualFileName == "not open") { abort = true; }
else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true; }
-
+ else { m->setQualFile(qualFileName); }
+
if((fastaFileName == "") && (qualFileName == "")){
fastaFileName = m->getFastaFile();
if (fastaFileName != "") { m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
m->openOutputFile(fastaReverseFileName, outFASTA);
while(!inFASTA.eof()){
- if (m->control_pressed) { inFASTA.close(); outFASTA.close(); remove(fastaReverseFileName.c_str()); return 0; }
+ if (m->control_pressed) { inFASTA.close(); outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; }
Sequence currSeq(inFASTA); m->gobble(inFASTA);
if (currSeq.getName() != "") {
m->openOutputFile(qualReverseFileName, outQual);
while(!inQual.eof()){
- if (m->control_pressed) { inQual.close(); outQual.close(); remove(qualReverseFileName.c_str()); return 0; }
+ if (m->control_pressed) { inQual.close(); outQual.close(); m->mothurRemove(qualReverseFileName); return 0; }
currQual = QualityScores(inQual); m->gobble(inQual);
currQual.flipQScores();
currQual.printQScores(outQual);
outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName);
}
- if (m->control_pressed) { remove(qualReverseFileName.c_str()); remove(fastaReverseFileName.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(qualReverseFileName); m->mothurRemove(fastaReverseFileName); return 0; }
//set fasta file as new current fastafile
string current = "";