sffinfocommand.h

   1 #ifndef SFFINFOCOMMAND_H
   2 #define SFFINFOCOMMAND_H
   3
   4 /*
   5  *  sffinfocommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 7/7/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14
  15
  16 /**********************************************************/
  17 struct CommonHeader {
  18         unsigned int magicNumber;
  19         string version;
  20         unsigned long int indexOffset;
  21         unsigned int indexLength;
  22         unsigned int numReads;
  23         unsigned short headerLength;
  24         unsigned short keyLength;
  25         unsigned short numFlowsPerRead;
  26         int flogramFormatCode;
  27         string flowChars; //length depends on number flow reads
  28         string keySequence; //length depends on key length
  29
  30         CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; }
  31         ~CommonHeader() { }
  32 };
  33 /**********************************************************/
  34 struct Header {
  35         unsigned short headerLength;
  36         unsigned short nameLength;
  37         unsigned int numBases;
  38         unsigned short clipQualLeft;
  39         unsigned short clipQualRight;
  40         unsigned short clipAdapterLeft;
  41         unsigned short clipAdapterRight;
  42         string name; //length depends on nameLength
  43
  44         Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
  45         ~Header() { }
  46 };
  47 /**********************************************************/
  48 struct seqRead {
  49         vector<unsigned short> flowgram;
  50         vector<unsigned int> flowIndex;
  51         string bases;
  52         vector<unsigned int> qualScores;
  53
  54         seqRead() { }
  55         ~seqRead() { }
  56 };
  57 /**********************************************************/
  58
  59 class SffInfoCommand : public Command {
  60
  61 public:
  62         SffInfoCommand(string);
  63         SffInfoCommand();
  64         ~SffInfoCommand();
  65         vector<string> getRequiredParameters();
  66         vector<string> getValidParameters();
  67         vector<string> getRequiredFiles();
  68         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  69         int execute();
  70         void help();
  71
  72 private:
  73         string sffFilename, outputDir, accnosName;
  74         vector<string> filenames, outputNames, accnosFileNames;
  75         bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
  76         set<string> seqNames;
  77         map<string, vector<string> > outputTypes;
  78
  79         int extractSffInfo(string, string);
  80         int readCommonHeader(ifstream&, CommonHeader&);
  81         int readHeader(ifstream&, Header&);
  82         int readSeqData(ifstream&, seqRead&, int, int);
  83
  84         int printCommonHeader(ofstream&, CommonHeader&);
  85         int printHeader(ofstream&, Header&);
  86         int printSffTxtSeqData(ofstream&, seqRead&, Header&);
  87         int printFlowSeqData(ofstream&, seqRead&, Header&);
  88         int printFastaSeqData(ofstream&, seqRead&, Header&);
  89         int printQualSeqData(ofstream&, seqRead&, Header&);
  90         int readAccnosFile(string);
  91
  92 };
  93
  94 /**********************************************************/
  95
  96 #endif
  97
  98