mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
30 lines
1.3 KiB
C
30 lines
1.3 KiB
C
#ifndef __PURGEDUPS__
|
|
#define __PURGEDUPS__
|
|
#include <stdio.h>
|
|
#include <stdint.h>
|
|
#include "kvec.h"
|
|
#include "kdq.h"
|
|
#include "Overlaps.h"
|
|
#include "Hash_Table.h"
|
|
#define COV_COUNT 1024
|
|
#define HOM_PEAK_RATE 1.25
|
|
#define HET_PEAK_RATE (HOM_PEAK_RATE*2)
|
|
#define ALTER_COV_THRES 0.9
|
|
#define REAL_ALTER_THRES 0.1
|
|
#define CHAIN_FILTER_RATE 0.7
|
|
|
|
void purge_dups(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources,
|
|
ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, kvec_asg_arc_t_warp* edge, float density,
|
|
uint32_t purege_minLen, int max_hang, int min_ovlp, long long bubble_dist, float drop_ratio,
|
|
uint32_t just_contain, uint32_t just_coverage, hap_cov_t *cov);
|
|
void fill_unitig(uint64_t* buffer, uint32_t bufferLen, asg_t* read_g, kvec_asg_arc_t_warp* edge,
|
|
uint32_t is_circle, uint64_t* rLen);
|
|
void get_contig_length(ma_ug_t *ug, asg_t *g, uint64_t* primaryLen, uint64_t* alterLen);
|
|
void enable_debug_mode(uint32_t mode);
|
|
hap_cov_t* init_hap_cov_t(ma_ug_t *ug, asg_t* read_g, ma_hit_t_alloc* sources, R_to_U* ruIndex, ma_hit_t_alloc* reverse_sources,
|
|
ma_sub_t *coverage_cut, int max_hang, int min_ovlp, hc_links* link);
|
|
void destory_hap_cov_t(hap_cov_t **x);
|
|
void chain_trans_ovlp(hap_cov_t *cov, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads, uint32_t targetBaseLen, uint32_t* xEnd);
|
|
|
|
|
|
#endif |