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         unsigned int magicNumber;
  21         char* version;
  22         unsigned long int indexOffset;
  23         unsigned int indexLength;
  24         unsigned int numReads;
  25         unsigned short headerLength;
  26         unsigned short keyLength;
  27         unsigned short numFlowsPerRead;
  28         char flogramFormatCode;
  29         char* flowChars; //length depends on number flow reads
  30         char* keySequence; //length depends on key length
  31
  32         CommonHeader(){ magicNumber=0; version=NULL; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; flowChars=NULL; keySequence=NULL; }
  33         ~CommonHeader() { if (version != NULL) { delete [] version; } if (flowChars != NULL) { delete [] flowChars; } if (keySequence != NULL) { delete [] keySequence; } }
  34 };
  35 /**********************************************************/
  36 struct Header {
  37         unsigned short headerLength;
  38         unsigned short nameLength;
  39         unsigned int numBases;
  40         unsigned short clipQualLeft;
  41         unsigned short clipQualRight;
  42         unsigned short clipAdapterLeft;
  43         unsigned short clipAdapterRight;
  44         char* name; //length depends on nameLength
  45
  46         Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; name=NULL; }
  47         ~Header() { if (name != NULL) { delete [] name; } }
  48 };
  49 /**********************************************************/
  50 struct seqRead {
  51         vector<unsigned short> flowgram;
  52         vector<unsigned int> flowIndex;
  53         char* bases;
  54         vector<unsigned int> qualScores;
  55
  56         seqRead() { bases=NULL; }
  57         ~seqRead() { if (bases != NULL) { delete [] bases; } }
  58 };
  59 /**********************************************************/
  60
  61 class SffInfoCommand : public Command {
  62
  63 public:
  64         SffInfoCommand(string);
  65         ~SffInfoCommand();
  66         int execute();
  67         void help();
  68
  69 private:
  70         string sffFilename, outputDir;
  71         vector<string> filenames, outputNames;
  72         bool abort;
  73
  74         int extractSffInfo(string, string);
  75         int readCommonHeader(ifstream&, CommonHeader*);
  76         int readHeader(ifstream&, Header*);
  77         int readSeqData(ifstream&, seqRead*, int, int);
  78
  79         int printCommonHeader(ofstream&, CommonHeader*, bool); //bool is debug mode
  80         int printHeader(ofstream&, Header*, bool);
  81         int printSeqData(ofstream&, seqRead*, bool);
  82
  83 };
  84
  85 /**********************************************************/
  86
  87 #endif
  88
  89