if(namesFileName != "") { weights = getWeights(); }
else if (countfile != "") {
CountTable ct;
- ct.readTable(countfile, false);
+ ct.readTable(countfile, false, false);
weights = ct.getNameMap();
}
//loop through and create all the processes you want
while (process != processors) {
- int pid = fork();
+ pid_t pid = fork();
if (pid > 0) {
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- num = driver(filename, qFileName, rFileName, summaryFileName + toString(getpid()) + ".temp", errorOutputFileName+ toString(getpid()) + ".temp", chimeraOutputFileName + toString(getpid()) + ".temp", lines[process], qLines[process], rLines[process]);
+ num = driver(filename, qFileName, rFileName, summaryFileName + m->mothurGetpid(process) + ".temp", errorOutputFileName+ m->mothurGetpid(process) + ".temp", chimeraOutputFileName + m->mothurGetpid(process) + ".temp", lines[process], qLines[process], rLines[process]);
//pass groupCounts to parent
ofstream out;
- string tempFile = filename + toString(getpid()) + ".info.temp";
+ string tempFile = filename + m->mothurGetpid(process) + ".info.temp";
m->openOutputFile(tempFile, out);
//output totalBases and totalMatches