1DEB928B08733DD80010E9CD /* Release */ = {
isa = XCBuildConfiguration;
buildSettings = {
- ARCHS = "$(NATIVE_ARCH_ACTUAL)";
+ ARCHS = "$(ARCHS_STANDARD_64_BIT)";
DEPLOYMENT_LOCATION = NO;
GCC_C_LANGUAGE_STANDARD = gnu99;
GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
"-lreadline",
);
PREBINDING = NO;
- SDKROOT = "";
+ SDKROOT = macosx10.5;
};
name = Release;
};
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { abort = true; }
+ if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") {
listfile = m->getListFile();
if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
//getting output filename
filename = listfile;
if (outputDir == "") { outputDir += m->hasPath(filename); }
-
+
filename = outputDir + m->getRootName(m->getSimpleName(filename));
filename = filename + "shared";
outputTypes["shared"].push_back(filename);
-
+
m->openOutputFile(filename, out);
pickedGroups = false;
temp = new ofstream;
filehandles[Groups[i]] = temp;
}
-
+
//set fileroot
fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
-
+
//clears file before we start to write to it below
for (int i=0; i<Groups.size(); i++) {
remove((fileroot + Groups[i] + ".rabund").c_str());
int SharedCommand::execute(){
try {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
//lookup.clear();
string errorOff = "no error";
//errorOff = "";