c_cpp/libgFileIO/_dist/libgFileIO.h

   1 // by Hu Xuesong
   2 #ifndef _G_FILEIO_H
   3 #define _G_FILEIO_H
   4
   5 #include <stdint.h>
   6
   7 #define GFIOCHRBASE 1
   8 #define GFIODIBBASE 2
   9
  10 #define G_HEADER_LENGTH 4
  11 #define G_TYPE_FAQC "FAQC"
  12 #define G_TYPE_GZ "0x1f0x8b0x08"
  13
  14
  15 struct __SeqFileObj;
  16 typedef ssize_t (G_ssize_t_oneIN)(struct __SeqFileObj * const);
  17 typedef void (G_p_oneIN)(struct __SeqFileObj * const);
  18
  19 typedef struct __SeqFileObj {
  20    size_t readlength,binNcount,binMallocedQQWord;
  21    const char *name, *comment, *seq, *qual;
  22    uint64_t *diBseq;   // 2bit, {A,C,G,T}={0,1,2,3}
  23    unsigned char *hexBQ;   // 0~63 for Quality, 128 for N, 64 for Eamss-masked or smallcase-masked
  24    G_ssize_t_oneIN *getNextSeq;
  25    G_p_oneIN *closefh;
  26    void *fobj;
  27    long datePos[1];   // [1] for item id, [0] for offset. For Text file, item id == 0.
  28    uint_fast8_t type;
  29 /* 1->hasBaseChr, 2->hasQchar, 4->hasBase2bit,
  30    8->hashexBQ or just array of {0,128} for N,
  31   16->Eamss bit set, 32->Q value not raw, after Eamss. */
  32 } SeqFileObj;   // We may support both FA/FQ and binary formats. So, object is a good thing.
  33
  34 SeqFileObj * inSeqFinit(const char * const, unsigned char);
  35
  36 void inSeqFdestroy(SeqFileObj * const);
  37
  38 #endif /* libgFileIO.h */