if (path == "") { parameters["file"] = inputDir + it->second; }
}
}
-
-
+
+ //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 = ""; }
+
//check for required parameters
flowFileName = validParameter.validFile(parameters, "flow", true);
flowFilesFileName = validParameter.validFile(parameters, "file", true);
}
else{
ofstream temp;
-
+
+ string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
+
//flow.files = 9 character offset
- compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+ compositeFASTAFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
m->openOutputFile(compositeFASTAFileName, temp);
temp.close();
- compositeNamesFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+ compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
m->openOutputFile(compositeNamesFileName, temp);
temp.close();
}
if (flowFileVector.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
}
else{
+ outputDir += m->hasPath(flowFileName);
flowFileVector.push_back(flowFileName);
}
-
-
- //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 = "";
- outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
- }
-
-
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
int j=4; //need to get past the first four bases
while(qualities[i][j] != -1){
- //cout << i << '\t' << j << '\t' << qualities[i][j] << endl;
qualityFile << qualities[i][j] << ' ';
+ if (j > qualities[i].size()) { break; }
j++;
-
}
qualityFile << endl;
}