Copied from SVN revision 4710 and adapted to Git.

[samtools.git] / bam_maqcns.h

diff --git a/bam_maqcns.h b/bam_maqcns.h
index 36704d7bce51104e1a8d73ed233f8ebd4b8ce582..6cc5355fc2db2b1b19e6a3d2d330306a240fa15a 100644 (file)
--- 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;
@@ -16,15 +16,17 @@ 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];