6 #include "bcftools/bcf.h"
8 #define B2B_INDEL_NULL 10000
10 typedef struct __bcf_callaux_t {
12 int openQ, extQ, tandemQ;
29 int a[5]; // alleles: ref, alt, alt2, alt3
30 int n, n_alleles, shift, ori_ref, unseen;
39 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
40 void bcf_call_destroy(bcf_callaux_t *bca);
41 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
42 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
43 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
44 const bcf_callaux_t *bca, const char *ref);
45 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref);