}
- if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
+ if((i+1) % 100 == 0){ cout << (i+1) << endl; }
}
if(outputString != ""){ //output to file
delete buf;
}
- if((num) % 100 != 0){ cout << (num) << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
+ if((num) % 100 != 0){ cout << (num) << endl; }
return 0;
}
#endif
//report progress
- if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
}
//report progress
- if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
out.close();
//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){
- string filteredFasta = filename + toString(getpid()) + ".temp";
+ string filteredFasta = filename + m->mothurGetpid(process) + ".temp";
num = driverRunFilter(F, filteredFasta, filename, lines[process]);
//pass numSeqs to parent
ofstream out;
- string tempFile = filename + toString(getpid()) + ".num.temp";
+ string tempFile = filename + m->mothurGetpid(process) + ".num.temp";
m->openOutputFile(tempFile, out);
out << num << endl;
out.close();
Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
- if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (m->debug) { m->mothurOut("[DEBUG]: " + seq.getName() + " length = " + toString(seq.getAligned().length())); m->mothurOutEndLine();}
+ if (seq.getAligned().length() != alignmentLength) { m->mothurOut("[ERROR]: Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
if(trump != '*') { F.doTrump(seq); }
if(m->isTrue(vertical) || soft != 0) { F.getFreqs(seq); }
#endif
//report progress
- if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
}
//report progress
- if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
in.close();
return count;
cout.flush();
//report progress
- if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
+ if((i+1) % 100 == 0){ cout << (i+1) << endl; }
}
//report progress
- if((num) % 100 != 0){ cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
+ if((num) % 100 != 0){ cout << num << endl; }
return 0;
}
//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
num = driverCreateFilter(F, filename, lines[process]);
//write out filter counts to file
- filename += toString(getpid()) + "filterValues.temp";
+ filename += m->mothurGetpid(process) + "filterValues.temp";
ofstream out;
m->openOutputFile(filename, out);