} bam_maqcns_t;
typedef struct {
- int q_indel;
- float r_indel;
+ int q_indel; // indel sequencing error, phred scaled
+ float r_indel; // indel prior
+ float r_snp; // snp prior
// hidden parameters, unchangeable from command line
int mm_penalty, indel_err, ambi_thres;
} bam_maqindel_opt_t;