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expose purge_dups

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chhylp123
2020-04-18 00:45:47 -04:00
parent 85c57fd087
commit 7f6725ead3
6 changed files with 117 additions and 36 deletions
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Overlaps.cpp
+30 -24
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@@ -13223,9 +13223,11 @@ kvec_asg_arc_t_warp* new_rtg_edges)
delete_useless_nodes(ug);
if (asm_opt.flag & HA_F_PURGE_TRIO) {
purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang,
min_ovlp, bubble_dist, drop_ratio, 1);
if(asm_opt.purge_level_trio == 1)
{
purge_dups(*ug, read_g, coverage_cut, 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);
}
@@ -21975,7 +21977,7 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
kvec_asg_arc_t_warp* new_rtg_edges)
{
asg_t* nsg = (*ug)->g;
uint32_t v, n_vtx = nsg->n_seq, k, rId;
uint32_t v, n_vtx = nsg->n_seq, k, rId, just_contain;
ma_utg_t* u = NULL;
@@ -22001,20 +22003,22 @@ kvec_asg_arc_t_warp* new_rtg_edges)
tip_drop_ratio, stops_threshold, ruIndex, NULL, NULL, 0, 0, 0,
chimeric_rate, 0, 0, drop_ratio);
///delete_useless_nodes(ug);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
///deduplicate_advance(*ug, read_g, coverage_cut, sources, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, 1);
if(asm_opt.purge_level_primary > 0)
{
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,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist,
drop_ratio, just_contain);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
}
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
///enable_debug_mode(1);
purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang,
min_ovlp, bubble_dist, drop_ratio, 0);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
@@ -22026,16 +22030,18 @@ kvec_asg_arc_t_warp* new_rtg_edges)
renew_utg(ug, read_g, new_rtg_edges);
///debug_purge_dup = 1;
///deduplicate_advance(*ug, read_g, coverage_cut, sources, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, 0);
///delete_useless_nodes(ug);
///enable_debug_mode(0);
purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang,
min_ovlp, bubble_dist, drop_ratio, 0);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
if(asm_opt.purge_level_primary > 0)
{
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,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist,
drop_ratio, just_contain);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
}
n_vtx = read_g->n_seq;
for (v = 0; v < n_vtx; v++)