if (namefile != "") { nameMap = m->readNames(namefile); }
else if (countfile != "") {
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, true);
nameMap = ct.getNameMap();
}
getSummary(positions);
if (namefile != "") { nameMap = m->readNames(namefile); }
else if (countfile != "") {
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, true);
nameMap = ct.getNameMap();
}
getSummaryReport();
m->mothurRemove(outSummary+".temp");
}
- if (numFastaSeqs != count) { m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your contigs report file, quitting.\n"); m->control_pressed = true; }
+ if (numFastaSeqs != count) { m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your align report file, quitting.\n"); m->control_pressed = true; }
return count;
if (namefile != "") { nameMap = m->readNames(namefile); }
else if (countfile != "") {
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, true);
nameMap = ct.getNameMap();
}
getSummary(positions);
vector<int> longHomoPolymer;
vector<int> numNs;
- vector<unsigned long long> positions;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(fastafile, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
int pid;
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
- if (pid == 0) {
- driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[0]);
+ if (pid == 0) {
+ linePair tempLine(0, positions[positions.size()-1]);
+ driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, tempLine);
#else
int numSeqs = 0;
//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//check for groups that have been eliminated
CountTable ct;
if (ct.testGroups(goodCountFile)) {
- ct.readTable(goodCountFile);
+ ct.readTable(goodCountFile, true);
ct.printTable(goodCountFile);
}
#endif
//report progress
- if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); }
}
//report progress
- if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); }
goodFile.close();
}
//report progress
- if((i) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine(); }
+ if((i) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(i)+"\n"); }
}
return 1;