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# New files in the new upstream release.
[samtools.git]
/
bam_maqcns.h
diff --git
a/bam_maqcns.h
b/bam_maqcns.h
index 36704d7bce51104e1a8d73ed233f8ebd4b8ce582..291ae533c3c38cd152b3c9c8fa8e820386a3718d 100644
(file)
--- a/
bam_maqcns.h
+++ b/
bam_maqcns.h
@@
-3,11
+3,15
@@
#include "glf.h"
#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;
struct __bmc_aux_t;
typedef struct {
float het_rate, theta;
- int n_hap, cap_mapQ;
+ int n_hap, cap_mapQ
, errmod, min_baseQ
;
float eta, q_r;
double *fk, *coef;
float eta, q_r;
double *fk, *coef;
@@
-16,15
+20,17
@@
typedef struct {
} bam_maqcns_t;
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;
// 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];
char *s[2];
//
int gt, gl[2];