xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-10 00:10:56 +08:00
Code Issues Packages Projects Releases Wiki Activity

upadate man-page and readme

Browse Source
This commit is contained in:
Haoyu Cheng
2020-01-04 11:54:08 +08:00
parent 1e46798bfb
commit d8416873f3
7 changed files with 407 additions and 176 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Overlaps.h
+11 -10
View File
@@ -7,14 +7,14 @@
///#define MIN_OVERLAP_LEN 2000
///#define MIN_OVERLAP_LEN 500
///#define MIN_OVERLAP_LEN 50
#define MIN_OVERLAP_LEN 50
///#define MIN_OVERLAP_LEN 50
///#define MIN_OVERLAP_COVERAGE 1
#define MIN_OVERLAP_COVERAGE 0
#define MAX_HANG_LEN 1000
#define MAX_HANG_PRE 0.8
#define GAP_FUZZ 1000
#define MAX_SHORT_TIPS 3
#define MAX_BUBBLE_DIST 10000000
///#define MIN_OVERLAP_COVERAGE 0
///#define MAX_HANG_LEN 1000
///#define MAX_HANG_PRE 0.8
///#define GAP_FUZZ 1000
///#define MAX_SHORT_TIPS 3
///#define MAX_BUBBLE_DIST 10000000
#define SMALL_BUBBLE_SIZE (uint32_t)-1
//#define SMALL_BUBBLE_SIZE 1000
@@ -77,7 +77,7 @@ typedef struct {
void ma_hit_sub(int min_dp, ma_hit_t_alloc* sources, long long n_read, uint64_t* readLen,
long long mini_overlap_length, ma_sub_t** coverage_cut);
void ma_hit_cut(int min_dp, ma_hit_t_alloc* sources, long long n_read, uint64_t* readLen,
void ma_hit_cut(ma_hit_t_alloc* sources, long long n_read, uint64_t* readLen,
long long mini_overlap_length, ma_sub_t** coverage_cut);
void ma_hit_flt(ma_hit_t_alloc* sources, long long n_read, const ma_sub_t *coverage_cut,
int max_hang, int min_ovlp);
@@ -116,7 +116,7 @@ typedef struct { size_t n, m; uint64_t *a; } asg64_v;
#define MA_HT_TCONT (-3)
#define MA_HT_SHORT_OVLP (-4)
///in default, max_hang = 1000, int_frac = 0.05, min_ovlp = 2000
///in default, max_hang = 1000, int_frac = 0.8, min_ovlp = 50
static inline int ma_hit2arc(const ma_hit_t *h, int ql, int tl, int max_hang, float int_frac, int min_ovlp, asg_arc_t *p)
{
int32_t tl5, tl3, ext5, ext3, qs = (int32_t)h->qns;
@@ -135,6 +135,7 @@ static inline int ma_hit2arc(const ma_hit_t *h, int ql, int tl, int max_hang, fl
if (ext5 > max_hang || ext3 > max_hang || h->qe - qs < (h->qe - qs + ext5 + ext3) * int_frac)
return MA_HT_INT;
**/
///ext3 and ext5 should be always 0
if (ext5 > max_hang || ext3 > max_hang
|| h->qe - qs < (h->qe - qs + ext5 + ext3) * int_frac
|| h->te - h->ts < (h->te - h->ts + ext5 + ext3) * int_frac)
@@ -326,7 +327,7 @@ static inline int count_out_without_del(const asg_t *g, uint32_t v)
void build_string_graph_without_clean(
int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long n_read, uint64_t* readLen, long long mini_overlap_length,
long long max_hang_length, long long clean_round, long long pop_bubble_size,
long long max_hang_length, long long clean_round, long long gap_fuzz,
float min_ovlp_drop_ratio, float max_ovlp_drop_ratio, char* output_file_name,
long long bubble_dist, int read_graph, int write);