}
}
//**********************************************************************************************************************
+string MakeFastQCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "fastq") { outputFileName = "fastq"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeFastQCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
MakeFastQCommand::MakeFastQCommand(){
try {
abort = true; calledHelp = true;
fastafile = m->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setFastaFile(fastafile); }
qualfile = validParameter.validFile(parameters, "qfile", true);
if (qualfile == "not open") { abort = true; qualfile = ""; }
qualfile = m->getQualFile();
if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current qualfile and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setQualFile(qualfile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "fastq";
+ string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fastq");
outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
ofstream out;
qFile.close();
out.close();
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
try {
string qualScores;
- int controlChar = int('!');
+ int controlChar = int('@');
for (int i = 0; i < qual.size(); i++) {
int temp = qual[i] + controlChar;