X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fprob1.h;h=6f9315565ba1369626d185ac30fcab3502e611d7;hb=125ac895854cf760a04192a257a4279f2c541164;hp=35c794fa1f78d8cea6781cb158dafbfff3553b93;hpb=390bbfbca2df79acf521706409a258895dfe72b1;p=samtools.git

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index 35c794f..6f93155 100644
--- a/bcftools/prob1.h
+++ b/bcftools/prob1.h
@@ -7,12 +7,18 @@ 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;
-	double pc[4];
-	double g[3];
+	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 cmp[3], p_chi2, lrt; // used by contrast2()
 } bcf_p1rst_t;
 
+typedef struct {
+    double p[4];
+    int mq, depth, is_tested, d[4];
+} anno16_t;
+
 #define MC_PTYPE_FULL  1
 #define MC_PTYPE_COND2 2
 #define MC_PTYPE_FLAT  3
@@ -21,15 +27,20 @@ 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);
+    void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma);
+	int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
+    int call_multiallelic_gt(bcf1_t *b, bcf_p1aux_t *ma, double threshold, int var_only);
 	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
 }