//**********************************************************************************************************************
ScreenSeqsCommand::ScreenSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
ScreenSeqsCommand::ScreenSeqsCommand(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
int ScreenSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//if the user want to optimize we need to no the 90% mark
vector<unsigned long int> positions;
int start = time(NULL);
#ifdef USE_MPI
- int pid, end, numSeqsPerProcessor;
+ int pid, numSeqsPerProcessor;
int tag = 2001;
vector<unsigned long int> MPIPos;
outputNames.push_back(goodNameFile); outputTypes["name"].push_back(goodNameFile);
ofstream goodNameOut; m->openOutputFile(goodNameFile, goodNameOut);
-
+
while(!inputNames.eof()){
if (m->control_pressed) { goodNameOut.close(); inputNames.close(); remove(goodNameFile.c_str()); return 0; }
inputNames >> seqName >> seqList;
it = badSeqNames.find(seqName);
-
+
if(it != badSeqNames.end()){
badSeqNames.erase(it);
if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str()); remove(goodGroupFile.c_str()); return 0; }
inputGroups >> seqName >> group;
-
+
it = badSeqGroups.find(seqName);
if(it != badSeqGroups.end()){
}
}
}
-
+
+
return 0;
}