X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_mcns.h;h=6f1a3109b666da3c59dd056922135513ad38faf3;hb=82c492c6e173dddc6876304b5bd14119ae9566fa;hp=a86fc1ddbd62e575ffeca6d2d59917e0b7e2f9a6;hpb=e23eb12b5f2c9b50b7db68b9aa972e50155540eb;p=samtools.git

diff --git a/bam_mcns.h b/bam_mcns.h
index a86fc1d..6f1a310 100644
--- 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
 }