typedef struct __bcf_callaux_t {
int capQ, min_baseQ;
- int openQ, extQ, tandemQ;
+ 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];
} bcf_callaux_t;
typedef struct {
- int depth, qsum[4];
+ int depth, ori_depth, 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 anno[16], depth;
+ int anno[16], depth, ori_depth;
uint8_t *PL;
} bcf_call_t;