projects
/
samtools.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Uploading 0.1.18-1 to unstable.
[samtools.git]
/
bam2bcf.h
diff --git
a/bam2bcf.h
b/bam2bcf.h
index 26b022c08e89e3597bd6e400690d42bd7ecabe38..4af080c4753b2070192bec5e04e16174ca5bb5f8 100644
(file)
--- a/
bam2bcf.h
+++ b/
bam2bcf.h
@@
-9,7
+9,9
@@
typedef struct __bcf_callaux_t {
int capQ, min_baseQ;
typedef struct __bcf_callaux_t {
int capQ, min_baseQ;
- int openQ, extQ, tandemQ;
+ int openQ, extQ, tandemQ; // for indels
+ int min_support; // for collecting indel candidates
+ double min_frac; // for collecting indel candidates
// for internal uses
int max_bases;
int indel_types[4];
// for internal uses
int max_bases;
int indel_types[4];
@@
-24,6
+26,7
@@
typedef struct {
int depth, ori_depth, qsum[4];
int anno[16];
float p[25];
int depth, ori_depth, qsum[4];
int anno[16];
float p[25];
+ int mvd[3]; // mean variant distance, number of variant reads, average read length
} bcf_callret1_t;
typedef struct {
} bcf_callret1_t;
typedef struct {
@@
-31,6
+34,7
@@
typedef struct {
int n, n_alleles, shift, ori_ref, unseen;
int anno[16], depth, ori_depth;
uint8_t *PL;
int n, n_alleles, shift, ori_ref, unseen;
int anno[16], depth, ori_depth;
uint8_t *PL;
+ float vdb; // variant distance bias
} bcf_call_t;
#ifdef __cplusplus
} bcf_call_t;
#ifdef __cplusplus