namefile = validParameter.validFile(parameters, "name", false);
if (namefile == "not found") { namefile = ""; }
-
else {
m->splitAtDash(namefile, namefileNames);
PhyloSummary* taxaSum;
if (hasCount) {
ct = new CountTable();
- ct->readTable(countfileNames[s]);
+ ct->readTable(countfileNames[s], true);
taxaSum = new PhyloSummary(taxonomyFileName, ct);
taxaSum->summarize(tempTaxonomyFile);
}else {
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
num += pDataArray[i]->count;
+ if (pDataArray[i]->count != pDataArray[i]->end) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
+ }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
#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"); }
inFASTA.close();
outTax.close();