//**********************************************************************************************************************
TrimSeqsCommand::TrimSeqsCommand(){
try {
+ abort = true;
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
}else if (pid == 0){
driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (trimQFile + toString(getpid()) + ".temp"), (scrapQFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, qualNames, lines[process], qLines[process]);
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
//force parent to wait until all the processes are done
//seach for filePos of each first name in the qfile and save in qfileFilePos
ifstream inQual;
m->openInputFile(qfilename, inQual);
-
+
string input;
while(!inQual.eof()){
input = m->getline(inQual);
}
inQual.close();
+
if (firstSeqNames.size() != 0) {
for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();