c_cpp/readscorr/gFileIO.h

   1 // by Hu Xuesong
   2 #ifndef _G_FILEIO_H
   3 #define _G_FILEIO_H
   4
   5 #include "gFileType.h"  // for file ID
   6 #include <stdint.h>     // uint64_t
   7 //#include "sdleft.h"
   8
   9 #define GFIOCHRBASE 1
  10 #define GFIODIBBASE 2
  11
  12 #ifndef KSTRING_T
  13 #define KSTRING_T kstring_t
  14 typedef struct __kstring_t {
  15         size_t l, m;    // l for sequence length in base-pairs, m for malloc in bytes.
  16         char *s;        // for 2bit ATCG, 1bp=2bit; for 6bit quality, 1bp=6bit.
  17 } kstring_t;
  18 #endif  // Yes, it is the same as that in kseq.h
  19
  20 //typedef ssize_t (*G_ssize_t_oneIN)(void * const);
  21 //typedef void (*G_p_oneIN)(void * const);
  22 struct __SeqFileObj;
  23 typedef ssize_t (G_ssize_t_oneIN)(struct __SeqFileObj * const);
  24 typedef void (G_p_oneIN)(struct __SeqFileObj * const);
  25
  26 typedef struct __SeqFileObj {
  27    size_t readlength,binNcount,binMallocedQQWord;
  28    const char *name, *comment, *seq, *qual;
  29         // $ cdecl explain "char * const* name"
  30         // declare name as pointer to const pointer to char
  31    uint64_t *diBseq;   // 2bit, {A,C,G,T}={0,1,2,3}
  32    unsigned char *hexBQ;   // 0~63 for Quality, 128 for N, 64 for Eamss-masked or smallcase-masked
  33    //int (*getNextSeq)(void *);   // void * fh
  34    G_ssize_t_oneIN *getNextSeq;
  35    G_p_oneIN *closefh; // remember to close file handle
  36    //= void (*closefh)(struct __SeqFileObj * const);
  37    void *fobj;   // Not just FILE *fp
  38    long datePos[1];   // [1] for item id, [0] for offset. For Text file, item id == 0.
  39    //long datePosOffset,datePosItem;
  40    uint_fast8_t type;   // 1->hasBaseChr, 2->hasQchar, 4->hasBase2bit,
  41    // 8->hashexBQ or just array of {0,128} for N,
  42    // 16->Eamss bit set, 32->Q value not raw, after Eamss.
  43 } SeqFileObj;   // We may support both FA/FQ and binary formats. So, object is a good thing.
  44
  45 SeqFileObj * inSeqFinit(const char * const, unsigned char);
  46 //ssize_t inSeqFreadNext(SeqFileObj * const);
  47 int inSeqFseek(SeqFileObj * const, const fpos_t datePos[]);
  48 void inSeqFdestroy(SeqFileObj * const);
  49
  50 #endif /* gFileIO.h */