Release samtools-0.1.16 (r963:234)

[samtools.git] / bam_maqcns.h

diff --git a/bam_maqcns.h b/bam_maqcns.h
index 56fa9db3a907f3087d6e4d114d54623a87491634..291ae533c3c38cd152b3c9c8fa8e820386a3718d 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;
+       int n_hap, cap_mapQ, errmod, min_baseQ;
 
        float eta, q_r;
        double *fk, *coef;
@@ -16,15 +20,17 @@ 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;
 
 typedef struct {
        int indel1, indel2;
-       int cnt1, cnt2, cnt_ambi, cnt_anti;
+       int cnt1, cnt2, cnt_anti;
+       int cnt_ref, cnt_ambi;
        char *s[2];
        //
        int gt, gl[2];