#include "bgzf.h"
typedef BGZF *glfFile;
-#define GLF_TYPE_NORMAL 0
-#define GLF_TYPE_INDEL 1
-#define GLF_TYPE_END 15
+#define GLF3_RTYPE_END 0
+#define GLF3_RTYPE_SUB 1
+#define GLF3_RTYPE_INDEL 2
typedef struct {
- unsigned char ref_base:4, type:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
- unsigned char max_mapQ; /** maximum mapping quality */
- unsigned char lk[10]; /** log likelihood ratio, capped at 255 */
- unsigned min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
- unsigned offset; /** the first base in a chromosome has offset zero. */
+ uint8_t ref_base:4, rtype:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
+ uint8_t rms_mapQ; /** RMS mapping quality */
+ uint8_t lk[10]; /** log likelihood ratio, capped at 255 */
+ uint32_t min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
+ int32_t offset; /** the first base in a chromosome has offset zero. */
+ // for indel (lkHom1, lkHom2 and lkHet are the first three elements in lk[10])
+ int16_t indel_len[2];
+ int32_t max_len; // maximum indel len; will be modified by glf3_read1()
+ char *indel_seq[2];
} glf3_t;
typedef struct {
int32_t l_text;
uint8_t *text;
-} glf_header_t;
+} glf3_header_t;
#ifdef __cplusplus
extern "C" {
#endif
- glf_header_t *glf_header_init();
- glf_header_t *glf_header_read(glfFile fp);
- void glf_header_write(glfFile fp, const glf_header_t *h);
- void glf_header_destroy(glf_header_t *h);
- char *glf_ref_read(glfFile fp);
- void glf_ref_write(glfFile fp, const char *str);
+#define glf3_init1() ((glf3_t*)calloc(1, sizeof(glf3_t)))
+#define glf3_destroy1(g3) do { free((g3)->indel_seq[0]); free((g3)->indel_seq[1]); free(g3); } while (0)
+
+ glf3_header_t *glf3_header_init();
+ glf3_header_t *glf3_header_read(glfFile fp);
+ void glf3_header_write(glfFile fp, const glf3_header_t *h);
+ void glf3_header_destroy(glf3_header_t *h);
+ char *glf3_ref_read(glfFile fp, int *len);
+ void glf3_ref_write(glfFile fp, const char *name, int len);
+ int glf3_write1(glfFile fp, const glf3_t *g3);
+ int glf3_read1(glfFile fp, glf3_t *g3);
#ifdef __cplusplus
}