6 #include "bcftools/bcf.h"
8 #define B2B_INDEL_NULL 10000
9 #define B2B_MAX_MNP 4 // cannot be larger than 4!!!
10 #define B2B_MNP_WIN 10
11 #define B2B_REF_INDEL (-1)
12 #define B2B_REF_MNP (-2)
14 typedef struct __bcf_callaux_t {
16 int openQ, extQ, tandemQ;
20 int maxins, indelreg, last_mnp_pos;
28 int depth, ori_depth, qsum[4];
34 int a[5]; // alleles: ref, alt, alt2, alt3
35 int n, n_alleles, shift, ori_ref, unseen; // ori_ref can be B2B_REF_INDEL/B2B_REF_MNP
36 int anno[16], depth, ori_depth;
44 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
45 void bcf_call_destroy(bcf_callaux_t *bca);
46 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
47 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
48 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
49 const bcf_callaux_t *bca, const char *ref);
50 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
52 int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref);