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 getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Make.contigs"; }
string getDescription() { return "description"; }
private:
bool abort, allFiles, createGroup;
- string outputDir, ffastqfile, rfastqfile, align, oligosfile;
+ string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, file;
float match, misMatch, gapOpen, gapExtend;
int processors, longestBase, threshold, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs;
vector<string> outputNames;
//vector<string> groupVector;
fastqRead readFastq(ifstream&, bool&);
- vector< vector<string> > readFastqFiles(int&);
+ vector< vector<string> > readFastqFiles(unsigned long int&);
bool checkReads(fastqRead&, fastqRead&);
int createProcesses(vector< vector<string> >, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
int driver(vector<string>, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);