X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fprob1.h;h=0a51a0ae2650f377f4fc48665109487687eb69cb;hp=b4f6a304ae49ff31f9ef9ae88db268cd3f01640e;hb=b301e959d73eee0955c57004f344f17af00703f4;hpb=c34624801b980425af68c3c431423c72b18c14fe

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index b4f6a30..0a51a0a 100644
--- a/bcftools/prob1.h
+++ b/bcftools/prob1.h
@@ -7,11 +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_folded, p_ref, p_var_folded, p_var;
+	int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
+	int ac; // ML alternative allele count
+	double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
 	double cil, cih;
-	double pc[4];
-	double g[3];
+	double cmp[3], p_chi2, lrt; // used by contrast2()
 } bcf_p1rst_t;
 
 #define MC_PTYPE_FULL  1
@@ -22,18 +22,19 @@ 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(const bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
+	int bcf_p1_cal(const bcf1_t *b, int do_contrast, 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
 
+	int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10]);
+
 #ifdef __cplusplus
 }
 #endif