6 #include "bcftools/bcf.h"
8 #define BAM2BCF_INDELREG_THRES 13
10 typedef struct __bcf_callaux_t {
11 int max_bases, capQ, min_baseQ;
12 int openQ, extQ, tandemQ;
20 float indelreg, ins_len, del_len;
27 int a[5]; // alleles: ref, alt, alt2, alt3
28 int n, n_alleles, shift, ori_ref, unseen;
37 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
38 void bcf_call_destroy(bcf_callaux_t *bca);
39 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r);
40 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
41 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP);
42 int bcf_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r);