m->mothurOut("DONE.");
m->mothurOutEndLine(); cout.flush();
- m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(rdb->referenceSeqs.size()) + " sequences."); m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(templateSequences.size()) + " sequences."); m->mothurOutEndLine();
}
#endif
}
else if(method == "suffix") { search = new SuffixDB(numSeqs); }
- else if(method == "blast") { search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch); }
+ else if(method == "blast") { search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, ""); }
else {
m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
m->mothurOutEndLine();
method = s;
if(method == "suffix") { search = new SuffixDB(); }
- else if(method == "blast") { search = new BlastDB(); }
+ else if(method == "blast") { search = new BlastDB(""); }
else { search = new KmerDB(); }