if(namesFileName != "") { weights = getWeights(); }
else if (countfile != "") {
CountTable ct;
- ct.readTable(countfile, false);
+ ct.readTable(countfile, false, false);
weights = ct.getNameMap();
}
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
string sname = ""; nameStream >> sname;
sname = sname.substr(1);
- for (int i = 0; i < sname.length(); i++) {
- if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
- }
+ m->checkName(sname);
map<string, int>::iterator it = firstSeqNames.find(sname);
istringstream nameStream(input);
string sname = ""; nameStream >> sname;
- for (int i = 0; i < sname.length(); i++) {
- if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
- }
+ m->checkName(sname);
map<string, int>::iterator it = firstSeqNamesReport.find(sname);