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 #define SFF_MAGIC   0x2e736666 /* ".sff" */
  16 #define SFF_VERSION "\0\0\0\1"
  17
  18 /**********************************************************/
  19 struct CommonHeader {
  20         uint32_t magicNumber;
  21         char* version;
  22         uint64_t indexOffset;
  23         uint32_t indexLength;
  24         uint32_t numReads;
  25         uint16_t headerLength;
  26         uint16_t keyLength;
  27         uint16_t numFlowsPerRead;
  28         uint8_t flogramFormatCode;
  29         char* flowChars; //length depends on number flow reads
  30         char* keySequence; //length depends on key length
  31
  32         CommonHeader() { magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; }
  33 };
  34 /**********************************************************/
  35 struct Header {
  36         unsigned short headerLength;
  37         unsigned short nameLength;
  38         unsigned int numBases;
  39         unsigned short clipQualLeft;
  40         unsigned short clipQualRight;
  41         unsigned short clipAdapterLeft;
  42         unsigned short clipAdapterRight;
  43         char* name; //length depends on nameLength
  44
  45         Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
  46 };
  47 /**********************************************************/
  48 struct seqRead {
  49         vector<unsigned short> flowgram;
  50         vector<unsigned int> flowIndex;
  51         char* bases;
  52         vector<unsigned int> qualScores;
  53 };
  54 /**********************************************************/
  55
  56 class SffInfoCommand : public Command {
  57
  58 public:
  59         SffInfoCommand(string);
  60         ~SffInfoCommand();
  61         int execute();
  62         void help();
  63
  64 private:
  65         string sffFilename, outputDir;
  66         vector<string> filenames, outputNames;
  67         bool abort;
  68
  69         int extractSffInfo(string, string);
  70         CommonHeader* readCommonHeader(ifstream&);
  71         Header* readHeader(ifstream&);
  72         seqRead* readSeqData(ifstream&, int, int);
  73
  74         int printCommonHeader(ofstream&, CommonHeader*, bool); //bool is debug mode
  75         int printHeader(ofstream&, Header*, bool);
  76         int printSeqData(ofstream&, seqRead*, bool);
  77
  78 };
  79
  80 /**********************************************************/
  81
  82 #endif
  83
  84