X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fprob1.h;h=b824c3c8375cd58dedb9bf3238d8cc4cb87d31a3;hb=674ffee7adcfc928f5039777180206fdebc5539b;hp=96beb0435806a693357f9d2dc4954857ed7d1065;hpb=f27c5d351576e00cece3708adcb386da61fe7b7f;p=samtools.git

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index 96beb04..b824c3c 100644
--- 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
 }