- char* tempIn = new char[8];
- *tempIn = '\0'; strncat(tempIn, "--input", 7);
- //strcpy(tempIn, "--input");
- cPara.push_back(tempIn);
- char* temp = new char[filename.length()+1];
- *temp = '\0'; strncat(temp, filename.c_str(), filename.length());
- //strcpy(temp, filename.c_str());
- cPara.push_back(temp);
-
- //add reference file
+ string outputFileName = filename.substr(1, filename.length()-2) + ".uchime_formatted";
+ //prepFile(filename.substr(1, filename.length()-2), outputFileName);
+ //prepFile(filename, outputFileName);
+ /******************************************/
+ ifstream in23;
+ pDataArray->m->openInputFile((filename.substr(1, filename.length()-2)), in23);
+
+ ofstream out23;
+ pDataArray->m->openOutputFile(outputFileName, out23);
+
+ while (!in23.eof()) {
+ if (pDataArray->m->control_pressed) { break; }
+
+ Sequence seq(in23); pDataArray->m->gobble(in23);
+
+ if (seq.getName() != "") { seq.printSequence(out23); }
+ }
+ in23.close();
+ out23.close();
+ /******************************************/
+
+ filename = outputFileName;
+ filename = "\"" + filename + "\"";
+
+ //add reference file