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apply coverage to purge_dups

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chhylp123
2020-07-06 10:02:03 -04:00
parent 428cc01d10
commit 2e56ef7db5
4 changed files with 368 additions and 19 deletions
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Overlaps.cpp
+4 -3
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@@ -13274,7 +13274,7 @@ kvec_asg_arc_t_warp* new_rtg_edges)
if(asm_opt.purge_level_trio == 1)
{
purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges,
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist,
drop_ratio, 1);
delete_useless_nodes(ug);
@@ -22080,7 +22080,7 @@ kvec_asg_arc_t_warp* new_rtg_edges)
just_contain = 0;
if(asm_opt.purge_level_primary == 1) just_contain = 1;
purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges,
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist,
drop_ratio, just_contain);
delete_useless_nodes(ug);
@@ -22102,7 +22102,7 @@ kvec_asg_arc_t_warp* new_rtg_edges)
just_contain = 0;
if(asm_opt.purge_level_primary == 1) just_contain = 1;
purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges,
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist,
drop_ratio, just_contain);
delete_useless_nodes(ug);
@@ -22559,6 +22559,7 @@ long long rescue_threshold)
}
long long get_coverage(ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, uint64_t n_read)
{
uint64_t i, j;