if (namefile != "") { nameMap = m->readNames(namefile); }
else if (countfile != "") {
CountTable ct;
- ct.readTable(countfile, false);
+ ct.readTable(countfile, false, false);
nameMap = ct.getNameMap();
}
double meanstartPosition, meanendPosition, meanseqLength, meanambigBases, meanlongHomoPolymer;
- meanstartPosition /= (double) size; meanendPosition /= (double) size; meanlongHomoPolymer /= (double) size; meanseqLength /= (double) size; meanambigBases /= (double) size;
+ meanstartPosition = meanStartPosition / (double) size; meanendPosition = meanEndPosition /(double) size; meanlongHomoPolymer = meanLongHomoPolymer / (double) size; meanseqLength = meanSeqLength / (double) size; meanambigBases = meanAmbigBases /(double) size;
int ptile0_25 = int(size * 0.025);
int ptile25 = int(size * 0.250);
bool done = false;
int count = 0;
-
+
+
while (!done) {
if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
ambigBases.push_back(current.getAmbigBases());
longHomoPolymer.push_back(current.getLongHomoPolymer());
}
-
count++;
outSummary << current.getName() << '\t';
outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
//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 = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
+ num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + m->mothurGetpid(process) + ".temp", lines[process]);
//pass numSeqs to parent
ofstream out;
- string tempFile = fastafile + toString(getpid()) + ".num.temp";
+ string tempFile = fastafile + m->mothurGetpid(process) + ".num.temp";
m->openOutputFile(tempFile, out);
out << num << endl;