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fix misassemblies

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chhylp123
2021-03-20 18:36:02 -04:00
parent e6e6dbf7b3
commit ede6ccef00
5 changed files with 210 additions and 286 deletions
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Overlaps.h
+6 -7
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@@ -1006,7 +1006,7 @@ typedef struct{
void resolve_tangles(ma_ug_t *src, asg_t *read_g, ma_hit_t_alloc* reverse_sources, long long minLongUntig,
long long maxShortUntig, float l_untig_rate, float max_node_threshold, R_to_U* ruIndex, uint32_t trio_flag,
float drop_ratio);
void adjust_utg_advance(asg_t *sg, ma_ug_t *ug, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex);
void adjust_utg_advance(asg_t *sg, ma_ug_t *ug, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, bub_label_t* b_mask_t);
void rescue_contained_reads_aggressive(ma_ug_t *i_ug, asg_t *r_g, ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp, uint32_t chainLenThres, uint32_t is_bubble_check,
uint32_t is_primary_check, kvec_asg_arc_t_warp* new_rtg_edges, kvec_t_u32_warp* new_rtg_nodes, bub_label_t* b_mask_t);
@@ -1051,9 +1051,6 @@ typedef struct{
typedef struct{
kvec_t(hc_linkeage) a;
kvec_t(uint64_t) enzymes;
kvec_t(bed_in) bed;
///uint32_t* u_idx;
///uint64_t r_num;
} hc_links;
@@ -1062,9 +1059,11 @@ typedef struct{
kvec_t(uint32_t) iDXs;
kvec_t(uint32_t) rescue_hom;
uint32_t* u_idx;
uint32_t r_num;
uint8_t* is_het;
uint32_t r_num, u_num;
uint32_t chain_num;
uint32_t l0_chain, l1_chain;
kvec_t(bed_in) bed;
}trans_chain;
typedef struct {
@@ -1090,7 +1089,7 @@ typedef struct{
hc_edge *a;
}hc_edge_warp;
void init_hc_links(hc_links* link, uint64_t ug_num, uint64_t r_num);
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);
@@ -1102,7 +1101,7 @@ 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, hc_links* link, 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);
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,