string getCommandName() { return "make.contigs"; }
string getCommandCategory() { return "Sequence Processing"; }
//commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
- string getHelpString();
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Make.contigs"; }
string getDescription() { return "description"; }
contigScores.push_back(scores1[ABaseMap[i]]);
if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[i]]; }
}else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below threshold. In that case eliminate base
- if (scores2[BBaseMap[i]] >= pDataArray->threshold)) {
+ if (scores2[BBaseMap[i]] >= pDataArray->threshold) {
contig += seq2[i];
contigScores.push_back(scores2[BBaseMap[i]]);
}