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;