backup commit

[samtools.git] / bcftools / prob1.h

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index d34a75f56de8e08efa49aa414ef1c5e896ae83a0..6f9315565ba1369626d185ac30fcab3502e611d7 100644 (file)
--- a/bcftools/prob1.h
+++ b/bcftools/prob1.h
@@ -7,10 +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;
+       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
@@ -19,12 +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);
+       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
 }