X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fprob1.h;fp=bcftools%2Fprob1.h;h=3f89dda5fafb59278e8e60cadcd82fe46fb0eaf0;hp=b4f6a304ae49ff31f9ef9ae88db268cd3f01640e;hb=fa217aa47313e2535cbd2d4bb034cfd405162662;hpb=c34624801b980425af68c3c431423c72b18c14fe

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index b4f6a30..3f89dda 100644
--- a/bcftools/prob1.h
+++ b/bcftools/prob1.h
@@ -7,10 +7,10 @@ struct __bcf_p1aux_t;
 typedef struct __bcf_p1aux_t bcf_p1aux_t;
 
 typedef struct {
-	int rank0;
+	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 pc[4];
+	double cmp[3], p_chi2; // used by contrast2()
 	double g[3];
 } bcf_p1rst_t;
 
@@ -22,7 +22,7 @@ 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);
@@ -30,7 +30,6 @@ extern "C" {
 	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