#define BAM2BCF_H
#include <stdint.h>
-#include "bcf.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;
- uint64_t sum_Q2;
- float p[25], esum[5];
+ float indelreg, ins_len, del_len;
+ int 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 depth, rmsQ;
+ int anno[16], depth;
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);
- int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b);
+ 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
}