X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=bam_maqcns.h;h=2c94fec066b25552b6008f28b8c129f5672cccc5;hp=5d410ef9fda607ba3f02a925522c4aa59864cf25;hb=635998cfe030da5f3dbec42a6daa3ca82fa5c871;hpb=d97f59c04fe0e183a66ad5b2f24a39a4b92f7f25

diff --git a/bam_maqcns.h b/bam_maqcns.h
index 5d410ef..2c94fec 100644
--- a/bam_maqcns.h
+++ b/bam_maqcns.h
@@ -16,13 +16,19 @@ typedef struct {
 } bam_maqcns_t;
 
 typedef struct {
+	int q_indel;
+	float r_indel;
+	// 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;
-	char *s1, *s2;
+	char *s[2];
+	//
+	int gt, gl[2];
+	int q_cns, q_ref;
 } bam_maqindel_ret_t;
 
 #ifdef __cplusplus