X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_maqcns.h;h=28733a5dbd8f467105d736bc4ffa1919be4d9e56;hb=5c4ef838b286eeb6fffc7c41ffbb776281963c8e;hp=2c94fec066b25552b6008f28b8c129f5672cccc5;hpb=635998cfe030da5f3dbec42a6daa3ca82fa5c871;p=samtools.git

diff --git a/bam_maqcns.h b/bam_maqcns.h
index 2c94fec..28733a5 100644
--- a/bam_maqcns.h
+++ b/bam_maqcns.h
@@ -3,11 +3,15 @@
 
 #include "glf.h"
 
+#define BAM_ERRMOD_MAQ2 0
+#define BAM_ERRMOD_MAQ  1
+#define BAM_ERRMOD_SOAP 2
+
 struct __bmc_aux_t;
 
 typedef struct {
 	float het_rate, theta;
-	int n_hap;
+	int n_hap, cap_mapQ, errmod;
 
 	float eta, q_r;
 	double *fk, *coef;
@@ -16,15 +20,17 @@ typedef struct {
 } bam_maqcns_t;
 
 typedef struct {
-	int q_indel;
-	float r_indel;
+	int q_indel; // indel sequencing error, phred scaled
+	float r_indel; // indel prior
+	float r_snp; // snp prior
 	// hidden parameters, unchangeable from command line
 	int mm_penalty, indel_err, ambi_thres;
 } bam_maqindel_opt_t;
 
 typedef struct {
 	int indel1, indel2;
-	int cnt1, cnt2, cnt_ambi, cnt_anti;
+	int cnt1, cnt2, cnt_anti;
+	int cnt_ref, cnt_ambi;
 	char *s[2];
 	//
 	int gt, gl[2];
@@ -44,7 +50,8 @@ extern "C" {
 	uint32_t glf2cns(const glf1_t *g, int q_r);
 
 	bam_maqindel_opt_t *bam_maqindel_opt_init();
-	bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref);
+	bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref,
+									 int _n_types, int *_types);
 	void bam_maqindel_ret_destroy(bam_maqindel_ret_t*);
 
 #ifdef __cplusplus