//**********************************************************************************************************************
SplitAbundCommand::SplitAbundCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["name"] = tempOutNames;
//**********************************************************************************************************************
SplitAbundCommand::SplitAbundCommand(string option) {
try {
- 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 SplitAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (listfile != "") { //you are using a listfile to determine abundance
if (outputDir == "") { outputDir = m->hasPath(listfile); }
if (accnos) { writeAccnos(tag); }
if (fastafile != "") { parseFasta(tag); }
}
-
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }