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Starting the work on next package update.
[samtools.git]
/
bcftools
/
prob1.h
diff --git
a/bcftools/prob1.h
b/bcftools/prob1.h
index 6d9d28e3cee6c7d0a66efbd5314912ac511cd384..0a51a0ae2650f377f4fc48665109487687eb69cb 100644
(file)
--- a/
bcftools/prob1.h
+++ b/
bcftools/prob1.h
@@
-7,11
+7,11
@@
struct __bcf_p1aux_t;
typedef struct __bcf_p1aux_t bcf_p1aux_t;
typedef struct {
typedef struct __bcf_p1aux_t bcf_p1aux_t;
typedef struct {
- int rank0;
- double f_em, f_exp, f_flat, p_ref;
+ int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
+ int ac; // ML alternative allele count
+ double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
double cil, cih;
double cil, cih;
- double pc[4];
- double g[3];
+ double cmp[3], p_chi2, lrt; // used by contrast2()
} bcf_p1rst_t;
#define MC_PTYPE_FULL 1
} bcf_p1rst_t;
#define MC_PTYPE_FULL 1
@@
-22,16
+22,18
@@
typedef struct {
extern "C" {
#endif
extern "C" {
#endif
- bcf_p1aux_t *bcf_p1_init(int n);
+ bcf_p1aux_t *bcf_p1_init(int n
, uint8_t *ploidy
);
void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
void bcf_p1_destroy(bcf_p1aux_t *ma);
void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
void bcf_p1_destroy(bcf_p1aux_t *ma);
- int bcf_p1_cal(
bcf1_t *b
, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
+ int bcf_p1_cal(
const bcf1_t *b, int do_contrast
, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
void bcf_p1_dump_afs(bcf_p1aux_t *ma);
int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
void bcf_p1_dump_afs(bcf_p1aux_t *ma);
int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
- long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3]);
int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
+ void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called
+
+ int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10]);
#ifdef __cplusplus
}
#ifdef __cplusplus
}