+
+ accnosName = validParameter.validFile(parameters, "accnos", false);
+ if (accnosName == "not found") { accnosName = ""; }
+ else {
+ hasAccnos = true;
+ m->splitAtDash(accnosName, accnosFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < accnosFileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = m->hasPath(accnosFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { accnosFileNames[i] = inputDir + accnosFileNames[i]; }
+ }
+
+ ifstream in;
+ int ableToOpen = m->openInputFile(accnosFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(accnosFileNames[i]);
+ m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ accnosFileNames[i] = tryPath;
+ }
+ }
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(accnosFileNames[i]);
+ m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ accnosFileNames[i] = tryPath;
+ }
+ }
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ accnosFileNames.erase(accnosFileNames.begin()+i);
+ i--;
+ }
+ }
+
+ //make sure there is at least one valid file left
+ if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ if (hasAccnos) {
+ if (accnosFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide a accnos file, you must have one for each sff file."); m->mothurOutEndLine(); }
+ }
+
+ string temp = validParameter.validFile(parameters, "qfile", false); if (temp == "not found"){ temp = "T"; }
+ qual = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ temp = "T"; }
+ fasta = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "flow", false); if (temp == "not found"){ temp = "F"; }
+ flow = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found"){ temp = "T"; }
+ trim = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "sfftxt", false);
+ if (temp == "not found") { temp = "F"; sfftxt = false; sfftxtFilename = ""; }
+ else if (m->isTrue(temp)) { sfftxt = true; sfftxtFilename = ""; }
+ else {
+ //you are a filename
+ if (inputDir != "") {
+ map<string,string>::iterator it = parameters.find("sfftxt");
+ //user has given a template file
+ if(it != parameters.end()){
+ string path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["sfftxt"] = inputDir + it->second; }
+ }
+ }
+
+ sfftxtFilename = validParameter.validFile(parameters, "sfftxt", true);
+ if (sfftxtFilename == "not found") { sfftxtFilename = ""; }
+ else if (sfftxtFilename == "not open") { sfftxtFilename = ""; }
+ }
+
+ if ((sfftxtFilename == "") && (filenames.size() == 0)) { m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true; }