#include "glf.h"
+#define BAM_ERRMOD_MAQ2 0
+#define BAM_ERRMOD_MAQ 1
+#define BAM_ERRMOD_SOAP 2
+
struct __bmc_aux_t;
typedef struct {
float het_rate, theta;
- int n_hap, cap_mapQ, is_soap;
+ int n_hap, cap_mapQ, errmod, min_baseQ;
float eta, q_r;
double *fk, *coef;
} 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;