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#ifndef BAM2BCF_H
#define BAM2BCF_H
#include <stdint.h>
#include "errmod.h"
#include "bcftools/bcf.h"
#define B2B_INDEL_NULL 10000
#define B2B_FMT_DP 0x1
#define B2B_FMT_SP 0x2
#define B2B_FMT_DV 0x4
typedef struct __bcf_callaux_t {
int capQ, min_baseQ;
int openQ, extQ, tandemQ; // for indels
int min_support, max_support; // for collecting indel candidates
double min_frac, max_frac; // for collecting indel candidates
int per_sample_flt; // indel filtering strategy
int *ref_pos, *alt_pos, npos; // for ReadPosBias
// for internal uses
int max_bases;
int indel_types[4];
int maxins, indelreg;
int read_len;
char *inscns;
uint16_t *bases;
errmod_t *e;
void *rghash;
} bcf_callaux_t;
typedef struct {
int depth, n_supp, ori_depth, qsum[4];
unsigned int anno[16];
float p[25];
} bcf_callret1_t;
typedef struct {
int a[5]; // alleles: ref, alt, alt2, alt3
float qsum[4];
int n, n_alleles, shift, ori_ref, unseen;
int n_supp; // number of supporting non-reference reads
unsigned int anno[16], depth, ori_depth;
uint8_t *PL;
float vdb; // variant distance bias
float read_pos_bias;
struct { float avg, var; int dp; } read_pos;
} bcf_call_t;
#ifdef __cplusplus
extern "C" {
#endif
bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
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, bcf_callaux_t *bca, 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 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);
#ifdef __cplusplus
}
#endif
#endif
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