X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fprob1.h;h=eb0b145285715c54d997693c449b5262462cb904;hb=70c740facc966321754c6bfcc6d61ea056480638;hp=3f89dda5fafb59278e8e60cadcd82fe46fb0eaf0;hpb=d382711a770f67a72b9af3bfd98a88fbced34f64;p=samtools.git

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index 3f89dda..eb0b145 100644
--- a/bcftools/prob1.h
+++ b/bcftools/prob1.h
@@ -8,12 +8,17 @@ typedef struct __bcf_p1aux_t bcf_p1aux_t;
 
 typedef struct {
 	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;
+	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; // used by contrast2()
-	double g[3];
+	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
@@ -26,13 +31,17 @@ extern "C" {
 	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);
+    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 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
 
+	int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10]);
+
 #ifdef __cplusplus
 }
 #endif