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r215: prepare for list-based binning

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Heng Li
2020-04-10 00:12:19 -04:00
parent 7a35bd7fcc
commit f32bfc904a
6 changed files with 50 additions and 33 deletions
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Overlaps.cpp
+8 -8
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@@ -22786,7 +22786,7 @@ 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 (!((asm_opt.pat_index && asm_opt.mat_index)))
if (!ha_opt_triobin(&asm_opt))
{
tri_flag += asg_arc_del_triangular_advance(sg, bubble_dist);
///remove the cross at the bubble carefully, just remove inexact cross
@@ -24105,7 +24105,7 @@ 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 (!((asm_opt.pat_index && asm_opt.mat_index)))
if (!ha_opt_triobin(&asm_opt))
{
///remove isoloated single read
tri_flag += asg_arc_del_triangular_advance(r_g, bubble_dist);
@@ -24376,7 +24376,7 @@ 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 (!((asm_opt.pat_index && asm_opt.mat_index)))
if (!ha_opt_triobin(&asm_opt))
{
///remove isoloated single read
tri_flag += asg_arc_del_triangular_advance(r_g, bubble_dist);
@@ -24754,7 +24754,7 @@ 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 (!((asm_opt.pat_index && asm_opt.mat_index)))
if (!ha_opt_triobin(&asm_opt))
{
///remove isoloated single read
tri_flag += asg_arc_del_triangular_advance(r_g, bubble_dist);
@@ -26312,7 +26312,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
// -1, "clean");
if ((asm_opt.pat_index && asm_opt.mat_index))
if (ha_opt_triobin(&asm_opt))
{
drop_edges_by_trio(sources, n_read);
}
@@ -26401,7 +26401,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_identify_simple_bubbles_multi(sg, 0);
///asg_arc_del_short_diploid_unclean_exact(sg, drop_ratio, sources);
if((asm_opt.pat_index && asm_opt.mat_index))
if (ha_opt_triobin(&asm_opt))
{
asg_arc_del_short_diploid_by_exact_trio(sg, asm_opt.max_short_tip, sources);
}
@@ -26414,7 +26414,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
asg_arc_identify_simple_bubbles_multi(sg, 1);
if((asm_opt.pat_index && asm_opt.mat_index))
if (ha_opt_triobin(&asm_opt))
{
asg_arc_del_short_diploid_by_length_trio(sg, drop_ratio, asm_opt.max_short_tip, reverse_sources,
asm_opt.max_short_tip, 1, 1, 0, 0, ruIndex);
@@ -26493,7 +26493,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
// rescue_no_coverage_aggressive(sg, sources, reverse_sources, &coverage_cut, ruIndex, max_hang_length,
// mini_overlap_length, bubble_dist, 10);
if ((asm_opt.pat_index && asm_opt.mat_index))
if (ha_opt_triobin(&asm_opt))
{
char *buf = (char*)calloc(strlen(output_file_name) + 25, 1);
sprintf(buf, "%s.dip", output_file_name);