#define BAM2BCF_H
#include <stdint.h>
-#include "bcf.h"
+#include "bcftools/bcf.h"
struct __bcf_callaux_t;
typedef struct __bcf_callaux_t bcf_callaux_t;
typedef struct {
- int depth;
+ int depth, d[4], ed[4];
uint64_t sum_Q2;
- float p[16], esum[4];
+ float p[25], esum[5];
} bcf_callret1_t;
typedef struct {
- int a[4]; // alleles: ref, alt, alt2, alt3
- int n, n_alleles, shift, ori_ref;
- int depth, rmsQ;
+ int a[5]; // alleles: ref, alt, alt2, alt3
+ int n, n_alleles, shift, ori_ref, unseen;
+ int d[4], ed[4], depth, rmsQ;
uint8_t *PL;
} bcf_call_t;
extern "C" {
#endif
- bcf_callaux_t *bcf_call_init(double theta);
+ 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);