for(int i=0;i<tempFASTAFileNames.size();i++){
for(int j=0;j<tempFASTAFileNames[i].size();j++){
if (tempFASTAFileNames[i][j] != "") {
- tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
+ tempFASTAFileNames[i][j] += m->mothurGetpid(process) + ".temp";
m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
}
}
}
num = driver(files[process],
- outputFasta + toString(getpid()) + ".temp",
- outputScrapFasta + toString(getpid()) + ".temp",
- outputMisMatches + toString(getpid()) + ".temp",
+ outputFasta + m->mothurGetpid(process) + ".temp",
+ outputScrapFasta + m->mothurGetpid(process) + ".temp",
+ outputMisMatches + m->mothurGetpid(process) + ".temp",
tempFASTAFileNames, process, group);
//pass groupCounts to parent
ofstream out;
- string tempFile = toString(getpid()) + ".num.temp";
+ string tempFile = m->mothurGetpid(process) + ".num.temp";
m->openOutputFile(tempFile, out);
out << num << endl;
if (createFileGroup || createOligosGroup) {
num++;
//report progress
- if((num) % 1000 == 0){ m->mothurOut(toString(num)); m->mothurOutEndLine(); }
+ if((num) % 1000 == 0){ m->mothurOutJustToScreen(toString(num)); m->mothurOutEndLine(); }
}
//report progress
count++;
//report progress
- if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 10000 == 0){ m->mothurOutJustToScreen(toString(count)); m->mothurOutEndLine(); }
//}
}
}
if (uniques.size() != 0) {
for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
+ if (m->control_pressed) { break; }
m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
}
for (map<string, pairFastqRead>:: iterator it = pairUniques.begin(); it != pairUniques.end(); it++) {
+ if (m->control_pressed) { break; }
m->mothurOut("[WARNING]: did not find paired read for " + (it->first).substr(1) + ", ignoring.\n");
}
m->mothurOutEndLine();
vector<int> qualScores = convertQual(quality);
+ m->checkName(name);
read.name = name;
read.sequence = sequence;
read.scores = qualScores;
else { uniquePrimers.insert(tempPair); }
if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); } }
-
primers[indexPrimer]=newPrimer; indexPrimer++;
primerNameVector.push_back(group);
}else if(type == "BARCODE"){