6 #include "bcftools/bcf.h"
8 #define B2B_INDEL_NULL 10000
10 #define B2B_FMT_DP 0x1
11 #define B2B_FMT_SP 0x2
12 #define B2B_FMT_DV 0x4
14 typedef struct __bcf_callaux_t {
16 int openQ, extQ, tandemQ; // for indels
17 int min_support; // for collecting indel candidates
18 double min_frac; // for collecting indel candidates
30 int depth, n_supp, ori_depth, qsum[4];
33 int mvd[3]; // mean variant distance, number of variant reads, average read length
37 int a[5]; // alleles: ref, alt, alt2, alt3
38 int n, n_alleles, shift, ori_ref, unseen;
39 int n_supp; // number of supporting non-reference reads
40 int anno[16], depth, ori_depth;
42 float vdb; // variant distance bias
49 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
50 void bcf_call_destroy(bcf_callaux_t *bca);
51 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
52 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
53 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
54 const bcf_callaux_t *bca, const char *ref);
55 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,