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 GLF3_RTYPE_END 0
16 #define GLF3_RTYPE_SUB 1
17 #define GLF3_RTYPE_INDEL 2
20 uint8_t ref_base:4, rtype:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
21 uint8_t rms_mapQ; /** RMS mapping quality */
22 uint8_t lk[10]; /** log likelihood ratio, capped at 255 */
23 uint32_t min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
24 int32_t offset; /** the first base in a chromosome has offset zero. */
25 // for indel (lkHom1, lkHom2 and lkHet are the first three elements in lk[10])
27 int32_t max_len; // maximum indel len; will be modified by glf3_read1()
40 #define glf3_init1() ((glf3_t*)calloc(1, sizeof(glf3_t)))
41 #define glf3_destroy1(g3) do { free((g3)->indel_seq[0]); free((g3)->indel_seq[1]); free(g3); } while (0)
43 glf3_header_t *glf3_header_init();
44 glf3_header_t *glf3_header_read(glfFile fp);
45 void glf3_header_write(glfFile fp, const glf3_header_t *h);
46 void glf3_header_destroy(glf3_header_t *h);
47 char *glf3_ref_read(glfFile fp, int *len);
48 void glf3_ref_write(glfFile fp, const char *name, int len);
49 int glf3_write1(glfFile fp, const glf3_t *g3);
50 int glf3_read1(glfFile fp, glf3_t *g3);