X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_maqcns.h;h=6cc5355fc2db2b1b19e6a3d2d330306a240fa15a;hp=2a82aeee8057f5992570d0896a1621b9116057cd;hb=cefa18095b2479339b08111936313066ec548657;hpb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a

diff --git a/bam_maqcns.h b/bam_maqcns.h
index 2a82aee..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;
@@ -16,8 +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;