vector<string> setParameters();
string getCommandName() { return "shhh.flows"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
- string getCitation() { return "http://www.mothur.org/wiki/Shhh.flows"; }
+ 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.\nQuince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT (2009). Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 6:639.\nhttp://www.mothur.org/wiki/Shhh.flows"; }
string getDescription() { return "shhh.flows"; }
vector<string> flowFileVector;
vector<string> parseFlowFiles(string);
- int driver(vector<string>, string, string, int, int);
+ int driver(vector<string>, string, string);
int createProcesses(vector<string>);
int getFlowData(string, vector<string>&, vector<int>&, vector<short>&, map<string, int>&, int&);
int getUniques(int, int, vector<short>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<double>&, vector<short>&);