5 #include "bcftools/bcf.h"
7 struct __bcf_callaux_t;
8 typedef struct __bcf_callaux_t bcf_callaux_t;
12 int dsum[2], d2sum[2];
18 int a[5]; // alleles: ref, alt, alt2, alt3
19 int n, n_alleles, shift, ori_ref, unseen;
20 int d[4], depth, rmsQ;
21 double davg[2], dstd[2];
29 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
30 void bcf_call_destroy(bcf_callaux_t *bca);
31 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r);
32 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
33 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b);