Imported Upstream version 0.1.14

[samtools.git] / bcftools / prob1.h

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index b4f6a304ae49ff31f9ef9ae88db268cd3f01640e..3f89dda5fafb59278e8e60cadcd82fe46fb0eaf0 100644 (file)
--- 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