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 getDescription() { return "shhh.flows"; }
linePair(int i, int j) : start(i), end(j) {}
};
- int abort;
+ bool abort, large;
string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName, compositeNamesFileName;
- int processors, maxIters;
+ int processors, maxIters, largeSize;
float cutoff, sigma, minDelta;
string flowOrder;
vector<double> jointLookUp;
vector<string> flowFileVector;
+ vector<string> parseFlowFiles(string);
int driver(vector<string>, string, string, int, int);
int createProcesses(vector<string>);
int getFlowData(string, vector<string>&, vector<int>&, vector<short>&, map<string, int>&, int&);
void writeQualities(int, int, string, vector<int>, vector<int>&, vector<int>&, vector<double>&, vector<short>&, vector<short>&, vector<int>&, vector<int>&, vector<string>&, vector<int>&, vector<vector<int> >&);
void writeSequences(string, int, int, string, vector<int>, vector<short>&, vector<string>&, vector<vector<int> >&, vector<int>&);
void writeNames(string, int, string, vector<int>, vector<string>&, vector<vector<int> >&, vector<int>&);
- void writeGroups(string, int, vector<string>&);
+ void writeGroups(string, string, int, vector<string>&);
void writeClusters(string, int, int, vector<int>, vector<int>&, vector<short>&, vector<string>&, vector<vector<int> >&, vector<int>&, vector<int>&, vector<short>&);
void getSingleLookUp();