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chhylp123
2020-10-26 11:01:48 -04:00
parent b2b4624cea
commit 0cc02035c5
6 changed files with 390 additions and 6 deletions
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Overlaps.cpp
+24 -4
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@@ -9,6 +9,7 @@
#include "Hash_Table.h"
#include "Correct.h"
#include "Purge_Dups.h"
#include "hic.h"
uint32_t debug_purge_dup = 0;
@@ -11630,6 +11631,21 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
}
void output_hic_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
{
kvec_asg_arc_t_warp new_rtg_edges;
kv_init(new_rtg_edges.a);
ma_ug_t *ug = NULL;
ug = ma_ug_gen(sg);
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp);
hic_analysis(ug);
ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a);
}
void merge_unitig_content(ma_utg_t* collection, ma_ug_t* ug, asg_t* read_g, kvec_asg_arc_t_warp* edge)
{
if(collection->m == 0) return;
@@ -23738,7 +23754,7 @@ void pre_clean(ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, asg_t *sg, long
///remove isoloated single read
tri_flag += asg_arc_del_single_node_directly(sg, asm_opt.max_short_tip, sources);
if (!ha_opt_triobin(&asm_opt))
if ((!ha_opt_triobin(&asm_opt))&&(!ha_opt_hic(&asm_opt)))
{
tri_flag += asg_arc_del_triangular_advance(sg, bubble_dist);
///remove the cross at the bubble carefully, just remove inexact cross
@@ -25057,7 +25073,7 @@ kvec_t_u32_warp* new_rtg_nodes)
int tri_flag = 0;
///remove very simple circle
tri_flag += asg_arc_del_simple_circle_untig(sources, coverage_cut, r_g, 100, 0);
if (!ha_opt_triobin(&asm_opt))
if ((!ha_opt_triobin(&asm_opt))&&(!ha_opt_hic(&asm_opt)))
{
///remove isoloated single read
tri_flag += asg_arc_del_triangular_advance(r_g, bubble_dist);
@@ -25328,7 +25344,7 @@ kvec_asg_arc_t_warp* new_rtg_edges)
int tri_flag = 0;
///remove very simple circle
tri_flag += asg_arc_del_simple_circle_untig(sources, coverage_cut, r_g, 100, 0);
if (!ha_opt_triobin(&asm_opt))
if ((!ha_opt_triobin(&asm_opt))&&(!ha_opt_hic(&asm_opt)))
{
///remove isoloated single read
tri_flag += asg_arc_del_triangular_advance(r_g, bubble_dist);
@@ -25706,7 +25722,7 @@ uint32_t is_bubble_check, uint32_t is_primary_check)
int tri_flag = 0;
///remove very simple circle
tri_flag += asg_arc_del_simple_circle_untig(sources, coverage_cut, r_g, 100, 0);
if (!ha_opt_triobin(&asm_opt))
if ((!ha_opt_triobin(&asm_opt))&&(!ha_opt_hic(&asm_opt)))
{
///remove isoloated single read
tri_flag += asg_arc_del_triangular_advance(r_g, bubble_dist);
@@ -27450,6 +27466,10 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
reverse_sources, bubble_dist, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang_length, mini_overlap_length);
}
else if(ha_opt_hic(&asm_opt))
{
output_hic_graph(sg, coverage_cut, output_file_name, sources, ruIndex, max_hang_length, mini_overlap_length);;
}
else
{