xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-04 14:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r249: make max overlap error rate CLI options

Browse Source
This commit is contained in:
Heng Li
2020-05-06 01:16:50 -04:00
parent 331e437c72
commit 3364a29b87
6 changed files with 56 additions and 49 deletions
Download Patch File Download Diff File Expand all files Collapse all files
CommandLines.h
+13 -9
View File
@@ -3,18 +3,20 @@
#include <pthread.h>
#define HA_VERSION "0.5-dirty-r248"
#define HA_VERSION "0.5-dirty-r249"
#define VERBOSE 0
#define HA_F_NO_HPC 0x1
#define HA_F_NO_KMER_FLT 0x2
#define HA_F_VERBOSE_GFA 0x4
#define HA_F_WRITE_EC 0x8
#define HA_F_WRITE_PAF 0x10
#define HA_F_SKIP_TRIOBIN 0x20
#define HA_F_NO_HPC 0x1
#define HA_F_NO_KMER_FLT 0x2
#define HA_F_VERBOSE_GFA 0x4
#define HA_F_WRITE_EC 0x8
#define HA_F_WRITE_PAF 0x10
#define HA_F_SKIP_TRIOBIN 0x20
#define HA_F_PURGE_CONTAIN 0x40
#define HA_F_PURGE_JOIN 0x80
#define HA_F_PURGE_JOIN 0x80
#define HA_MIN_OV_DIFF 0.02 // min sequence divergence in an overlap
typedef struct {
int flag;
@@ -28,7 +30,9 @@ typedef struct {
int k_mer_length;
int mz_win;
int bf_shift;
float high_factor; // coverage cutoff set to high_factor*hom_cov
double high_factor; // coverage cutoff set to high_factor*hom_cov
double max_ov_diff_ec;
double max_ov_diff_final;
int hom_cov;
int max_n_chain; // fall-back max number of chains to consider
int k_mer_min_freq;