6 #define BAM_ERRMOD_MAQ2 0
7 #define BAM_ERRMOD_MAQ 1
8 #define BAM_ERRMOD_SOAP 2
13 float het_rate, theta;
14 int n_hap, cap_mapQ, errmod, min_baseQ;
19 struct __bmc_aux_t *aux;
23 int q_indel; // indel sequencing error, phred scaled
24 float r_indel; // indel prior
25 float r_snp; // snp prior
26 // hidden parameters, unchangeable from command line
27 int mm_penalty, indel_err, ambi_thres;
32 int cnt1, cnt2, cnt_anti;
33 int cnt_ref, cnt_ambi;
44 bam_maqcns_t *bam_maqcns_init();
45 void bam_maqcns_prepare(bam_maqcns_t *bm);
46 void bam_maqcns_destroy(bam_maqcns_t *bm);
47 glf1_t *bam_maqcns_glfgen(int n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm);
48 uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm);
49 // return: cns<<28 | cns2<<24 | mapQ<<16 | cnsQ<<8 | cnsQ2
50 uint32_t glf2cns(const glf1_t *g, int q_r);
52 bam_maqindel_opt_t *bam_maqindel_opt_init();
53 bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref,
54 int _n_types, int *_types);
55 void bam_maqindel_ret_destroy(bam_maqindel_ret_t*);