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bam2bcf.h

#ifndef BAM2BCF_H
#define BAM2BCF_H

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

#define B2B_INDEL_NULL 10000

typedef struct __bcf_callaux_t {
      int capQ, min_baseQ;
      int openQ, extQ, tandemQ;
      // for internal uses
      int max_bases;
      int indel_types[4];
      int maxins, indelreg;
      char *inscns;
      uint16_t *bases;
      errmod_t *e;
      void *rghash;
} bcf_callaux_t;

typedef struct {
      int depth, ori_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, ori_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, 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,
                               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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