10 int n_hap, cap_mapQ, is_soap;
15 struct __bmc_aux_t *aux;
19 int q_indel; // indel sequencing error, phred scaled
20 float r_indel; // indel prior
21 float r_snp; // snp prior
22 // hidden parameters, unchangeable from command line
23 int mm_penalty, indel_err, ambi_thres;
28 int cnt1, cnt2, cnt_anti;
29 int cnt_ref, cnt_ambi;
40 bam_maqcns_t *bam_maqcns_init();
41 void bam_maqcns_prepare(bam_maqcns_t *bm);
42 void bam_maqcns_destroy(bam_maqcns_t *bm);
43 glf1_t *bam_maqcns_glfgen(int n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm);
44 uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm);
45 // return: cns<<28 | cns2<<24 | mapQ<<16 | cnsQ<<8 | cnsQ2
46 uint32_t glf2cns(const glf1_t *g, int q_r);
48 bam_maqindel_opt_t *bam_maqindel_opt_init();
49 bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref,
50 int _n_types, int *_types);
51 void bam_maqindel_ret_destroy(bam_maqindel_ret_t*);