added the haploid mode

[samtools.git] / bcftools / prob1.h

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index 35c794fa1f78d8cea6781cb158dafbfff3553b93..eb4dc9216c27358712c98ec6444f5ea249ad6242 100644 (file)
--- a/bcftools/prob1.h
+++ b/bcftools/prob1.h
@@ -8,7 +8,8 @@ typedef struct __bcf_p1aux_t bcf_p1aux_t;
 
 typedef struct {
        int rank0;
-       double f_em, f_exp, f_flat, p_ref;
+       double f_em, f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
+       double cil, cih;
        double pc[4];
        double g[3];
 } bcf_p1rst_t;
@@ -21,15 +22,16 @@ typedef struct {
 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);
-       int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
+       int bcf_p1_cal(const bcf1_t *b, 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);
-       long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3]);
        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
 
 #ifdef __cplusplus
 }