X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_maqcns.h;h=6cc5355fc2db2b1b19e6a3d2d330306a240fa15a;hp=36704d7bce51104e1a8d73ed233f8ebd4b8ce582;hb=049705238f6c2d4cdd79022e7bcf2cc7d83ba9c7;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906

diff --git a/bam_maqcns.h b/bam_maqcns.h
index 36704d7..6cc5355 100644
--- a/bam_maqcns.h
+++ b/bam_maqcns.h
@@ -7,7 +7,7 @@ struct __bmc_aux_t;
 
 typedef struct {
 	float het_rate, theta;
-	int n_hap, cap_mapQ;
+	int n_hap, cap_mapQ, is_soap;
 
 	float eta, q_r;
 	double *fk, *coef;
@@ -16,15 +16,17 @@ 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];