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, max_support; // for collecting indel candidates
18 double min_frac, max_frac; // for collecting indel candidates
19 int per_sample_flt; // indel filtering strategy
20 int *ref_pos, *alt_pos, npos; // for ReadPosBias
33 int depth, n_supp, ori_depth, qsum[4];
34 unsigned int anno[16];
39 int a[5]; // alleles: ref, alt, alt2, alt3
41 int n, n_alleles, shift, ori_ref, unseen;
42 int n_supp; // number of supporting non-reference reads
43 unsigned int anno[16], depth, ori_depth;
45 float vdb; // variant distance bias
47 struct { float avg, var; int dp; } read_pos;
54 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
55 void bcf_call_destroy(bcf_callaux_t *bca);
56 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
57 int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call);
58 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
59 const bcf_callaux_t *bca, const char *ref);
60 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,