15 struct __bmc_aux_t *aux;
19 int mm_penalty, indel_err, ambi_thres;
24 int cnt1, cnt2, cnt_ambi, cnt_anti;
32 bam_maqcns_t *bam_maqcns_init();
33 void bam_maqcns_prepare(bam_maqcns_t *bm);
34 void bam_maqcns_destroy(bam_maqcns_t *bm);
35 glf1_t *bam_maqcns_glfgen(int n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm);
36 uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm);
37 // return: cns<<28 | cns2<<24 | mapQ<<16 | cnsQ<<8 | cnsQ2
38 uint32_t glf2cns(const glf1_t *g, int q_r);
40 bam_maqindel_opt_t *bam_maqindel_opt_init();
41 bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref);
42 void bam_maqindel_ret_destroy(bam_maqindel_ret_t*);