X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_maqcns.h;h=6cc5355fc2db2b1b19e6a3d2d330306a240fa15a;hp=fa5489d13caad7c5c20489091302bfb5b2a5799d;hb=cb12a866906ec4ac644de0e658679261c82ab098;hpb=3a3b72190c04cb076438f5027e13fcf5ddee77be

diff --git a/bam_maqcns.h b/bam_maqcns.h
index fa5489d..6cc5355 100644
--- a/bam_maqcns.h
+++ b/bam_maqcns.h
@@ -16,8 +16,9 @@ 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;