#include "errmod.h"
#include "bcftools/bcf.h"
-#define B2B_INDEL_NULL 0x7fff
-#define B2B_MAX_MNP 4 // cannot be larger than 4!!!
-#define B2B_MNP_WIN 10
-#define B2B_REF_INDEL (-1)
-#define B2B_REF_MNP (-2)
+#define B2B_INDEL_NULL 10000
typedef struct __bcf_callaux_t {
int capQ, min_baseQ;
// for internal uses
int max_bases;
int indel_types[4];
- int maxins, indelreg, last_mnp_pos;
+ int maxins, indelreg;
char *inscns;
uint16_t *bases;
errmod_t *e;
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 anno[16], depth, ori_depth;
uint8_t *PL;
} bcf_call_t;
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);
- int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref);
#ifdef __cplusplus
}