bool abort;
string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy, countfile, contigsreport, summaryfile;
- int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria, minOverlap, oStart, oEnd, mismatches, maxN, maxInsert;
- float minSim, minScore;
+ int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, minOverlap, oStart, oEnd, mismatches, maxN, maxInsert;
+ float minSim, minScore, criteria;
vector<string> outputNames;
vector<string> optimize;
map<string, int> nameMap;
}
//report progress
- if((i+1) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(i+1)); pDataArray->m->mothurOutEndLine(); }
+ if((i+1) % 100 == 0){ pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(i+1)+"\n"); }
}
//report progress
- if((pDataArray->count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 100 != 0){ pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n"); }