* Merge from branches/dev/

[samtools.git] / bam_maqcns.h

diff --git a/bam_maqcns.h b/bam_maqcns.h
index 5d410ef9fda607ba3f02a925522c4aa59864cf25..2c94fec066b25552b6008f28b8c129f5672cccc5 100644 (file)
--- 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