//**********************************************************************************************************************
CatchAllCommand::CatchAllCommand(){
try {
+ abort = true; calledHelp = true;
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["csv"] = tempOutNames;
CatchAllCommand::CatchAllCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//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
int CatchAllCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//prepare full output directory
outputDir = m->getFullPathName(outputDir);
try {
ifstream in;
- m->openInputFile(file1, in);
+ int able = m->openInputFile(file1, in, "noerror");
+ if (able == 1) { m->mothurOut("[ERROR]: the catchall program did not run properly. Please check to make sure it is located in the same folder as your mothur executable.");m->mothurOutEndLine(); m->control_pressed = true; return 0; }
+
if (!in.eof()) {
string header = m->getline(in); m->gobble(in);