fixed a bug in realignment

[samtools.git] / bam_maqcns.h

diff --git a/bam_maqcns.h b/bam_maqcns.h
index fa5489d13caad7c5c20489091302bfb5b2a5799d..28733a5dbd8f467105d736bc4ffa1919be4d9e56 100644 (file)
--- a/bam_maqcns.h
+++ b/bam_maqcns.h
@@ -3,11 +3,15 @@
 
 #include "glf.h"
 
+#define BAM_ERRMOD_MAQ2 0
+#define BAM_ERRMOD_MAQ  1
+#define BAM_ERRMOD_SOAP 2
+
 struct __bmc_aux_t;
 
 typedef struct {
        float het_rate, theta;
-       int n_hap, cap_mapQ, is_soap;
+       int n_hap, cap_mapQ, errmod;
 
        float eta, q_r;
        double *fk, *coef;
@@ -16,8 +20,9 @@ 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;