7 typedef struct __bcf_p1aux_t bcf_p1aux_t;
10 int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
11 int ac; // ML alternative allele count
12 double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
14 double cmp[3], p_chi2, lrt; // used by contrast2()
17 #define MC_PTYPE_FULL 1
18 #define MC_PTYPE_COND2 2
19 #define MC_PTYPE_FLAT 3
25 bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy);
26 void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
27 void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
28 void bcf_p1_destroy(bcf_p1aux_t *ma);
29 int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
30 int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
31 void bcf_p1_dump_afs(bcf_p1aux_t *ma);
32 int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
33 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
34 void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called
36 int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10]);