tools/bioawk/addon.h

   1 #ifndef ADDON_H
   2 #define ADDON_H
   3
   4 /* do not change these values, as they are tied to col_def[][] in addon.c */
   5 #define BIO_NULL -1
   6 #define BIO_HDR   0
   7 #define BIO_BED   1
   8 #define BIO_SAM   2
   9 #define BIO_VCF   3
  10 #define BIO_GFF   4
  11 #define BIO_FASTX 5
  12
  13 #define BIO_SHOW_HDR 0x1
  14
  15 extern int bio_fmt, bio_flag;
  16 extern char *bio_hdr_chr;
  17
  18 int bio_get_fmt(const char *s);
  19 int bio_skip_hdr(const char *r);
  20 void bio_set_colnm(void);
  21
  22 int bio_getrec(char **pbuf, int *psize, int isrecord);
  23
  24 /* The following explains how to add a new function. 1) Add a function index
  25  * (e.g. #define BIO_FFOO 102) in addon.h. The integer index must be larger than
  26  * 14 in the current awk implementation (see also macros starting with "F"
  27  * defined in awk.h). 2) Add the function name and the function index in the
  28  * keywords array defined in lex.c. Remember to keep the array sorted. 3)
  29  * Implement the actual function in bio_func(). */
  30
  31 #define BIO_FAND      101
  32 #define BIO_FOR       102
  33 #define BIO_FXOR      103
  34 #define BIO_FLSHIFT   104 /* to add */
  35 #define BIO_FRSHIFT   105 /* to add */
  36 #define BIO_FCOMPL    106 /* to add */
  37
  38 #define BIO_FREVERSE  201
  39 #define BIO_FREVCOMP  202
  40 #define BIO_FGC       203
  41 #define BIO_FMEANQUAL 204
  42 #define BIO_FQUALCOUNT 205
  43 #define BIO_FTRIMQ    206
  44
  45
  46 struct Cell;
  47 struct Node;
  48
  49 struct Cell *bio_func(int f, struct Cell *x, struct Node **a);
  50
  51 #endif