Updated samtools to 0.1.19

[rsem.git] / sam / bcftools / prob1.h

diff --git a/sam/bcftools/prob1.h b/sam/bcftools/prob1.h
index 0a51a0ae2650f377f4fc48665109487687eb69cb..6f9315565ba1369626d185ac30fcab3502e611d7 100644 (file)
--- a/sam/bcftools/prob1.h
+++ b/sam/bcftools/prob1.h
@@ -14,6 +14,11 @@ typedef struct {
        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
@@ -26,7 +31,9 @@ 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);
+    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);