* added BED support to samtools view and mpileup and bcftools view

[samtools.git] / bcftools / prob1.h

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index 96beb0435806a693357f9d2dc4954857ed7d1065..b824c3c8375cd58dedb9bf3238d8cc4cb87d31a3 100644 (file)
--- a/bcftools/prob1.h
+++ b/bcftools/prob1.h
@@ -7,8 +7,11 @@ struct __bcf_p1aux_t;
 typedef struct __bcf_p1aux_t bcf_p1aux_t;
 
 typedef struct {
-       int rank0;
-       double f_em, f_exp, f_flat, p_ref, g[3];
+       int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
+       double f_em, f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
+       double cil, cih;
+       double cmp[3], p_chi2, f_em2[2]; // used by contrast2()
+       double g[3];
 } bcf_p1rst_t;
 
 #define MC_PTYPE_FULL  1
@@ -19,12 +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);
+       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
 }