//**********************************************************************************************************************
ChimeraBellerophonCommand::ChimeraBellerophonCommand(){
try {
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
//***************************************************************************************************************
ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
int ChimeraBellerophonCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int i = 0; i < fastaFileNames.size(); i++) {
MPI_File_open(MPI_COMM_WORLD, FileName, outMode, MPI_INFO_NULL, &outMPI); //comm, filename, mode, info, filepointer
MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
- numSeqs = chimera->print(outMPI, outMPIAccnos);
+ numSeqs = chimera->print(outMPI, outMPIAccnos, "");
MPI_File_close(&outMPI);
MPI_File_close(&outMPIAccnos);
ofstream out2;
m->openOutputFile(accnosFileName, out2);
- numSeqs = chimera->print(out, out2);
+ numSeqs = chimera->print(out, out2, "");
out.close();
out2.close();