X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_maqcns.h;h=fa5489d13caad7c5c20489091302bfb5b2a5799d;hp=36704d7bce51104e1a8d73ed233f8ebd4b8ce582;hb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906

diff --git a/bam_maqcns.h b/bam_maqcns.h
index 36704d7..fa5489d 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;
@@ -24,7 +24,8 @@ typedef struct {
 
 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];