SamTools_custom/bam2bcf.h at master · CosteaPaul/SamTools_custom · GitHub

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#ifndef BAM2BCF_H
#define BAM2BCF_H

#include <stdint.h>
#include "bcftools/bcf.h"

struct __bcf_callaux_t;
typedef struct __bcf_callaux_t bcf_callaux_t;

typedef struct {
	int depth, qsum[4];
	int anno[16];
	float p[25];
} bcf_callret1_t;

typedef struct {
	int a[5]; // alleles: ref, alt, alt2, alt3
	int n, n_alleles, shift, ori_ref, unseen;
	int anno[16], depth;
	uint8_t *PL;
} 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 /*4-bit*/, 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);

#ifdef __cplusplus
}
#endif

#endif