vector<string> setParameters();
string getCommandName() { return "shhh.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nQuince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38.\nhttp://www.mothur.org/wiki/Shhh.seqs"; }
string getDescription() { return "shhh.seqs"; }
MothurOut* m;
int start;
int end;
- int sigma, threadID;
+ int sigma, threadID, count;
vector<string> groups;
vector<string> mapfileNames;
sigma = s;
threadID = tid;
groups = gr;
+ count=0;
}
};
//precluster each group
for (int k = pDataArray->start; k < pDataArray->end; k++) {
+ pDataArray->count++;
+
int start = time(NULL);
if (pDataArray->m->control_pressed) { return 0; }