BGI/SOAPdenovo2/standardPregraph/inc/glf.h

   1
   2 #ifndef GLF_H_
   3 #define GLF_H_
   4
   5 typedef struct
   6 {
   7         unsigned char ref_base: 4, dummy: 4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
   8         unsigned char max_mapQ; /** maximum mapping quality */
   9         unsigned char lk[10];   /** log likelihood ratio, capped at 255 */
  10         unsigned min_lk: 8, depth: 24; /** minimum lk capped at 255, and the number of mapped reads */
  11 } glf1_t;
  12
  13 #include <stdint.h>
  14 #include "bgzf.h"
  15 typedef BGZF * glfFile;
  16
  17 #define GLF3_RTYPE_END   0
  18 #define GLF3_RTYPE_SUB   1
  19 #define GLF3_RTYPE_INDEL 2
  20
  21 typedef struct
  22 {
  23         uint8_t ref_base: 4, rtype: 4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
  24         uint8_t rms_mapQ; /** RMS mapping quality */
  25         uint8_t lk[10];   /** log likelihood ratio, capped at 255 */
  26         uint32_t min_lk: 8, depth: 24; /** minimum lk capped at 255, and the number of mapped reads */
  27         int32_t offset; /** the first base in a chromosome has offset zero. */
  28         // for indel (lkHom1, lkHom2 and lkHet are the first three elements in lk[10])
  29         int16_t indel_len[2];
  30         int32_t max_len; // maximum indel len; will be modified by glf3_read1()
  31         char * indel_seq[2];
  32 } glf3_t;
  33
  34 typedef struct
  35 {
  36         int32_t l_text;
  37         uint8_t * text;
  38 } glf3_header_t;
  39
  40 #ifdef __cplusplus
  41 extern "C" {
  42 #endif
  43
  44 #define glf3_init1() ((glf3_t*)calloc(1, sizeof(glf3_t)))
  45 #define glf3_destroy1(g3) do { free((g3)->indel_seq[0]); free((g3)->indel_seq[1]); free(g3); } while (0)
  46
  47         glf3_header_t * glf3_header_init();
  48         glf3_header_t * glf3_header_read ( glfFile fp );
  49         void glf3_header_write ( glfFile fp, const glf3_header_t * h );
  50         void glf3_header_destroy ( glf3_header_t * h );
  51         char * glf3_ref_read ( glfFile fp, int * len );
  52         void glf3_ref_write ( glfFile fp, const char * name, int len );
  53         int glf3_write1 ( glfFile fp, const glf3_t * g3 );
  54         int glf3_read1 ( glfFile fp, glf3_t * g3 );
  55
  56 #ifdef __cplusplus
  57 }
  58 #endif
  59
  60 #endif