1 #ifndef CLUSTERSPLITCOMMAND_H
2 #define CLUSTERSPLITCOMMAND_H
5 * clustersplitcommand.h
8 * Created by westcott on 5/19/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "rabundvector.hpp"
15 #include "sabundvector.hpp"
16 #include "listvector.hpp"
17 #include "cluster.hpp"
18 #include "sparsematrix.hpp"
21 class ClusterSplitCommand : public Command {
24 ClusterSplitCommand(string);
25 ClusterSplitCommand();
26 ~ClusterSplitCommand() {}
28 vector<string> setParameters();
29 string getCommandName() { return "cluster.split"; }
30 string getCommandCategory() { return "Clustering"; }
31 string getHelpString();
32 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"; }
33 string getDescription() { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
36 void help() { m->mothurOut(getHelpString()); }
39 vector<int> processIDS; //processid
40 vector<string> outputNames;
42 string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
43 double cutoff, splitcutoff;
44 int precision, length, processors, taxLevelCutoff;
45 bool print_start, abort, hard, large;
47 ofstream outList, outRabund, outSabund;
49 void printData(ListVector*);
50 int createProcesses(vector < vector < map<string, string> > >);
51 vector<string> cluster(vector< map<string, string> >, set<string>&);
52 int mergeLists(vector<string>, map<float, int>, ListVector*);
53 map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
54 int createMergedDistanceFile(vector< map<string, string> >);