mergesfffilecommand.h

   1 //
   2 //  mergesfffilecommand.h
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 1/31/14.
   6 //  Copyright (c) 2014 Schloss Lab. All rights reserved.
   7 //
   8
   9 #ifndef Mothur_mergesfffilecommand_h
  10 #define Mothur_mergesfffilecommand_h
  11
  12 #include "command.hpp"
  13
  14
  15 /**********************************************************/
  16 class MergeSfffilesCommand : public Command {
  17
  18 public:
  19         MergeSfffilesCommand(string);
  20         MergeSfffilesCommand();
  21         ~MergeSfffilesCommand(){}
  22
  23         vector<string> setParameters();
  24         string getCommandName()                 { return "merge.sfffiles";                                      }
  25         string getCommandCategory()             { return "Sequence Processing";         }
  26
  27         string getHelpString();
  28     string getOutputPattern(string);
  29         string getCitation() { return "http://www.mothur.org/wiki/merge.sfffiles"; }
  30         string getDescription()         { return "merge individual sfffiles into a single .sff file"; }
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35 private:
  36         string sffFilename, outputDir, file, currentFileName;
  37         vector<string> filenames, outputNames;
  38         bool abort;
  39     int numTotalReads, allFilesnumFlowReads, allFileskeyLength;
  40     string outputFile, outputFileHeader;
  41     vector<CommonHeader> commonHeaders;
  42
  43         //extract sff file functions
  44         int mergeSffInfo(string, ofstream&);
  45         int readCommonHeader(ifstream&, CommonHeader&);
  46         int readHeader(ifstream&, Header&);
  47         bool readSeqData(ifstream&, seqRead&, int, Header&, ofstream&);
  48         int decodeName(string&, string&, string&, string);
  49
  50         bool sanityCheck(Header&, seqRead&);
  51     int adjustCommonHeader();
  52     int readFile();
  53 };
  54
  55 /**********************************************************/
  56
  57 #endif