} bam_maqcns_t;
typedef struct {
+ int q_indel;
+ float r_indel;
+ // hidden parameters, unchangeable from command line
int mm_penalty, indel_err, ambi_thres;
} bam_maqindel_opt_t;
typedef struct {
int indel1, indel2;
int cnt1, cnt2, cnt_ambi, cnt_anti;
- char *s1, *s2;
+ char *s[2];
+ //
+ int gt, gl[2];
+ int q_cns, q_ref;
} bam_maqindel_ret_t;
#ifdef __cplusplus