supposedly this is THE correct implementation, but more testing is needed

[samtools.git] / bam_mcns.h

diff --git a/bam_mcns.h b/bam_mcns.h
index a86fc1ddbd62e575ffeca6d2d59917e0b7e2f9a6..6f1a3109b666da3c59dd056922135513ad38faf3 100644 (file)
--- a/bam_mcns.h
+++ b/bam_mcns.h
@@ -8,16 +8,15 @@ typedef struct __mc_aux_t mc_aux_t;
 
 typedef struct {
        // O(n)
-       int ref, alt;
+       int ref, alt, alt2;
        double f_em, f_naive, f_nielsen;
        // O(n^2)
-       double PD, p_ref, f_exp;
-       // O(n^3)
-       double f_map, p_map; // map=maximum a posterior
+       double p_ref, f_exp;
 } mc_rst_t;
 
 #define MC_PTYPE_FULL  1
 #define MC_PTYPE_COND2 2
+#define MC_PTYPE_FLAT  3
 
 #ifdef __cplusplus
 extern "C" {
@@ -28,6 +27,7 @@ extern "C" {
        void mc_destroy(mc_aux_t *ma);
        int mc_cal(int ref, int *n, const bam_pileup1_t **plp, mc_aux_t *ma, mc_rst_t *rst, int level);
        int mc_call_gt(const mc_aux_t *ma, double f0, int k);
+       void mc_dump_afs(mc_aux_t *ma);
 
 #ifdef __cplusplus
 }