5 unsigned char ref_base:4, dummy:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
6 unsigned char max_mapQ; /** maximum mapping quality */
7 unsigned char lk[10]; /** log likelihood ratio, capped at 255 */
8 unsigned min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
13 typedef BGZF *glfFile;
15 #define GLF_TYPE_NORMAL 0
16 #define GLF_TYPE_INDEL 1
17 #define GLF_TYPE_END 15
20 unsigned char ref_base:4, type:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
21 unsigned char max_mapQ; /** maximum mapping quality */
22 unsigned char lk[10]; /** log likelihood ratio, capped at 255 */
23 unsigned min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
24 unsigned pos; /** this is ***ZERO-BASED*** coordinate */
36 glf_header_t *glf_header_init();
37 glf_header_t *glf_header_read(glfFile fp);
38 void glf_header_write(glfFile fp, const glf_header_t *h);
39 void glf_header_destroy(glf_header_t *h);
40 char *glf_ref_read(glfFile fp);
41 void glf_ref_write(glfFile fp, const char *str);