countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { abort = true; countfile = ""; }
else if (countfile == "not found") { countfile = ""; }
- else { ct.readTable(countfile); m->setCountTableFile(countfile); }
+ else { ct.readTable(countfile, true); m->setCountTableFile(countfile); }
if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster.fragments command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
alignSeqs[i].active = 0;
}//end if active i
- if(i % 100 == 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
+ if(i % 100 == 0) { m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); }
}
- if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
+ if(numSeqs % 100 != 0) { m->mothurOutJustToScreen(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); }
string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));