if (temp.getName() != "") {
templateSequences.push_back(temp);
//save longest base
- if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; }
+ if (temp.getUnaligned().length() >= longest) { longest = temp.getUnaligned().length()+1; }
}
}
if (temp.getName() != "") {
templateSequences.push_back(temp);
//save longest base
- if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; }
+ if (temp.getUnaligned().length() >= longest) { longest = (temp.getUnaligned().length()+1); }
}
}
fastaFile.close();
-
#endif
numSeqs = templateSequences.size();
#endif
}
else if(method == "suffix") { search = new SuffixDB(numSeqs); }
- else if(method == "blast") { search = new BlastDB(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();