vector<string> setParameters();
string getCommandName() { return "cluster.split"; }
string getCommandCategory() { return "Clustering"; }
vector<string> setParameters();
string getCommandName() { return "cluster.split"; }
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Cluster.split"; }
string getDescription() { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
string getHelpString();
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Cluster.split"; }
string getDescription() { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
double cutoff, splitcutoff;
int precision, length, processors, taxLevelCutoff;
string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
double cutoff, splitcutoff;
int precision, length, processors, taxLevelCutoff;
- bool print_start, abort, hard, large;
+ bool print_start, abort, hard, large, classic;
time_t start;
ofstream outList, outRabund, outSabund;
void printData(ListVector*);
vector<string> createProcesses(vector< map<string, string> >, set<string>&);
vector<string> cluster(vector< map<string, string> >, set<string>&);
time_t start;
ofstream outList, outRabund, outSabund;
void printData(ListVector*);
vector<string> createProcesses(vector< map<string, string> >, set<string>&);
vector<string> cluster(vector< map<string, string> >, set<string>&);
+ string clusterFile(string, string, set<string>&, double&);
+ string clusterClassicFile(string, string, set<string>&, double&);
int mergeLists(vector<string>, map<float, int>, ListVector*);
map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
int createMergedDistanceFile(vector< map<string, string> >);
int mergeLists(vector<string>, map<float, int>, ListVector*);
map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
int createMergedDistanceFile(vector< map<string, string> >);