xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-06 02:08:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

update contig flipping

Browse Source
This commit is contained in:
chhylp123
2021-03-25 03:03:19 -04:00
parent 9e3e1e8bab
commit d89a630ff3
6 changed files with 1041 additions and 56 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Overlaps.h
+11 -4
View File
@@ -1064,6 +1064,9 @@ typedef struct{
uint32_t chain_num;
uint32_t l0_chain, l1_chain;
kvec_t(bed_in) bed;
kvec_t(uint32_t) topo_buf;
kvec_t(uint32_t) topo_res;
buf_t b_buf;
}trans_chain;
typedef struct {
@@ -1093,15 +1096,15 @@ void init_hc_links(hc_links* link, uint64_t ug_num, trans_chain* t_ch);
void destory_hc_links(hc_links* link);
uint64_t get_bub_pop_max_dist(asg_t *g, buf_t *b);
uint64_t get_bub_pop_max_dist_advance(asg_t *g, buf_t *b);
int asg_pop_bubble_primary_trio(ma_ug_t *ug, uint64_t* i_max_dist, uint32_t positive_flag, uint32_t negative_flag, hap_cov_t *cov);
int asg_pop_bubble_primary_trio(ma_ug_t *ug, uint64_t* i_max_dist, uint32_t positive_flag, uint32_t negative_flag, hap_cov_t *cov, uint32_t is_update_chain);
uint64_t asg_bub_pop1_primary_trio(asg_t *g, ma_ug_t *utg, uint32_t v0, uint64_t max_dist, buf_t *b, uint32_t positive_flag,
uint32_t negative_flag, uint32_t is_pop, uint64_t* path_base_len, uint64_t* path_nodes, hap_cov_t *cov);
uint32_t negative_flag, uint32_t is_pop, uint64_t* path_base_len, uint64_t* path_nodes, hap_cov_t *cov, uint32_t is_update_chain);
void adjust_utg_by_primary(ma_ug_t **ug, asg_t* read_g, float drop_rate,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, ma_sub_t* coverage_cut,
long long tipsLen, float tip_drop_ratio, long long stops_threshold,
R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp,
kvec_asg_arc_t_warp* new_rtg_edges, hap_cov_t *i_cov, bub_label_t* b_mask_t);
kvec_asg_arc_t_warp* new_rtg_edges, hap_cov_t *i_cov, bub_label_t* b_mask_t, uint32_t collect_p_trans);
ma_ug_t* copy_untig_graph(ma_ug_t *src);
ma_ug_t* output_trio_unitig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
uint8_t flag, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
@@ -1119,7 +1122,11 @@ inline int inter_interval(int a_s, int a_e, int b_s, int b_e, int* i_s, int* i_e
return 1;
}
inline uint32_t get_origin_uid(uint32_t v, trans_chain* t_ch)
{
if(t_ch->u_idx[v>>1] == (uint32_t)-1) return (uint32_t)-1;
return ((t_ch->u_idx[v>>1]>>1)<<1) + ((t_ch->u_idx[v>>1]^v)&1);
}
#define JUNK_COV 5