15 struct __bmc_aux_t *aux;
21 // hidden parameters, unchangeable from command line
22 int mm_penalty, indel_err, ambi_thres;
27 int cnt1, cnt2, cnt_ambi, cnt_anti;
38 bam_maqcns_t *bam_maqcns_init();
39 void bam_maqcns_prepare(bam_maqcns_t *bm);
40 void bam_maqcns_destroy(bam_maqcns_t *bm);
41 glf1_t *bam_maqcns_glfgen(int n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm);
42 uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm);
43 // return: cns<<28 | cns2<<24 | mapQ<<16 | cnsQ<<8 | cnsQ2
44 uint32_t glf2cns(const glf1_t *g, int q_r);
46 bam_maqindel_opt_t *bam_maqindel_opt_init();
47 bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref,
48 int _n_types, int *_types);
49 void bam_maqindel_ret_destroy(bam_maqindel_ret_t*);