makecontigscommand.h

   1 #ifndef Mothur_makecontigscommand_h
   2 #define Mothur_makecontigscommand_h
   3
   4 //
   5 //  makecontigscommand.h
   6 //  Mothur
   7 //
   8 //  Created by Sarah Westcott on 5/15/12.
   9 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
  10 //
  11
  12 #include "command.hpp"
  13
  14 struct fastqRead {
  15         vector<int> scores;
  16         string name;
  17         string sequence;
  18
  19         fastqRead() { name = ""; sequence = ""; scores.clear(); };
  20         fastqRead(string n, string s, vector<int> sc) : name(n), sequence(s), scores(sc) {};
  21         ~fastqRead() {};
  22 };
  23
  24 /**************************************************************************************************/
  25
  26 class MakeContigsCommand : public Command {
  27 public:
  28     MakeContigsCommand(string);
  29     MakeContigsCommand();
  30     ~MakeContigsCommand(){}
  31
  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"; }
  39
  40     int execute();
  41     void help() { m->mothurOut(getHelpString()); }
  42
  43 private:
  44     bool abort;
  45     string outputDir, ffastqfile, rfastqfile, align;
  46         float match, misMatch, gapOpen, gapExtend;
  47         int processors, longestBase;
  48     vector<string> outputNames;
  49
  50     fastqRead readFastq(ifstream&);
  51     vector< vector<string> > readFastqFiles(int&);
  52     bool checkReads(fastqRead&, fastqRead&);
  53 };
  54
  55 /**************************************************************************************************/
  56
  57
  58
  59
  60
  61
  62
  63 #endif