#define BAM2BCF_H
#include <stdint.h>
+#include "errmod.h"
#include "bcftools/bcf.h"
-struct __bcf_callaux_t;
-typedef struct __bcf_callaux_t bcf_callaux_t;
+#define BAM2BCF_INDELREG_THRES 13
+
+typedef struct __bcf_callaux_t {
+ int max_bases, capQ, min_baseQ;
+ int openQ, extQ, tandemQ;
+ // for internal uses
+ uint16_t *bases;
+ errmod_t *e;
+} bcf_callaux_t;
typedef struct {
- int depth, qsum[4];
+ int depth;
+ float indelreg, ins_len, del_len;
+ int qsum[4];
int anno[16];
float p[25];
} bcf_callret1_t;
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, bcf_callret1_t *bcr, int is_SP);
+ int bcf_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r);
#ifdef __cplusplus
}