1 #ifndef Mothur_makecontigscommand_h
2 #define Mothur_makecontigscommand_h
5 // makecontigscommand.h
8 // Created by Sarah Westcott on 5/15/12.
9 // Copyright (c) 2012 Schloss Lab. All rights reserved.
12 #include "command.hpp"
19 fastqRead() { name = ""; sequence = ""; scores.clear(); };
20 fastqRead(string n, string s, vector<int> sc) : name(n), sequence(s), scores(sc) {};
24 /**************************************************************************************************/
26 class MakeContigsCommand : public Command {
28 MakeContigsCommand(string);
30 ~MakeContigsCommand(){}
32 vector<string> setParameters();
33 string getCommandName() { return "make.contigs"; }
34 string getCommandCategory() { return "Sequence Processing"; }
35 //commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
36 string getHelpString();
37 string getCitation() { return "http://www.mothur.org/wiki/Make.contigs"; }
38 string getDescription() { return "description"; }
41 void help() { m->mothurOut(getHelpString()); }
45 string outputDir, ffastqfile, rfastqfile, align;
46 float match, misMatch, gapOpen, gapExtend;
47 int processors, longestBase;
48 vector<string> outputNames;
50 fastqRead readFastq(ifstream&);
51 vector< vector<string> > readFastqFiles(int&);
52 bool checkReads(fastqRead&, fastqRead&);
55 /**************************************************************************************************/