- int openQ, extQ, tandemQ;
+ int openQ, extQ, tandemQ; // for indels
+ int min_support; // for collecting indel candidates
+ double min_frac; // for collecting indel candidates
} bcf_callret1_t;
typedef struct {
int a[5]; // alleles: ref, alt, alt2, alt3
} bcf_callret1_t;
typedef struct {
int a[5]; // alleles: ref, alt, alt2, alt3
- int n, n_alleles, shift, ori_ref, unseen; // ori_ref can be B2B_REF_INDEL/B2B_REF_MNP
+ int n, n_alleles, shift, ori_ref, unseen;
+ int n_supp; // number of supporting non-reference reads
void bcf_call_destroy(bcf_callaux_t *bca);
int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
void bcf_call_destroy(bcf_callaux_t *bca);
int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
- int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
+ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
const bcf_callaux_t *bca, const char *ref);
int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
const void *rghash);
const bcf_callaux_t *bca, const char *ref);
int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
const void *rghash);