#include "errmod.h"
#include "bcftools/bcf.h"
-#define BAM2BCF_INDELREG_THRES 13
+#define B2B_INDEL_NULL 10000
+
+#define B2B_FMT_DP 0x1
+#define B2B_FMT_SP 0x2
+#define B2B_FMT_DV 0x4
typedef struct __bcf_callaux_t {
- int max_bases, capQ, min_baseQ;
- int openQ, extQ, tandemQ;
+ int capQ, min_baseQ;
+ int openQ, extQ, tandemQ; // for indels
+ int min_support; // for collecting indel candidates
+ double min_frac; // for collecting indel candidates
// 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, indelreg;
- float ins_len, del_len;
- int qsum[4];
+ int depth, n_supp, ori_depth, qsum[4];
int anno[16];
float p[25];
+ int mvd[3]; // mean variant distance, number of variant reads, average read length
} bcf_callret1_t;
typedef struct {
int a[5]; // alleles: ref, alt, alt2, alt3
int n, n_alleles, shift, ori_ref, unseen;
- int indelreg;
- float ins_len, del_len;
- int depth, anno[16];
+ int n_supp; // number of supporting non-reference reads
+ int anno[16], depth, ori_depth;
uint8_t *PL;
+ float vdb; // variant distance bias
} bcf_call_t;
#ifdef __cplusplus
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_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_call_combine_gap(int n, const bcf_callret1_t *calls, 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);
+ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
+ 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
}