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chhylp123
2020-06-08 17:51:36 -04:00
parent 97f6efc4da
commit 71f6c93d58
4 changed files with 52 additions and 39 deletions
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Overlaps.cpp
+41 -34
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@@ -13251,16 +13251,19 @@ kvec_asg_arc_t_warp* new_rtg_edges)
renew_utg(ug, read_g, new_rtg_edges);
rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
min_ovlp, 0, 0, 1, NULL);
if (!(asm_opt.flag & HA_F_BAN_POST_JOIN))
{
rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
min_ovlp, 0, 0, 1, NULL);
renew_utg(ug, read_g, new_rtg_edges);
renew_utg(ug, read_g, new_rtg_edges);
rescue_contained_reads_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
min_ovlp, 0, 10, 0, 1, NULL, NULL);
renew_utg(ug, read_g, new_rtg_edges);
rescue_contained_reads_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
min_ovlp, 0, 10, 0, 1, NULL, NULL);
renew_utg(ug, read_g, new_rtg_edges);
}
update_unitig_graph((*ug), read_g, reverse_sources, ruIndex, 1, flag, drop_rate);
update_hap_label(NULL, read_g);
@@ -22084,27 +22087,27 @@ kvec_asg_arc_t_warp* new_rtg_edges)
renew_utg(ug, read_g, new_rtg_edges);
}
rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
min_ovlp, 0, 0, 1, NULL);
renew_utg(ug, read_g, new_rtg_edges);
rescue_contained_reads_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
min_ovlp, 0, 10, 0, 1, NULL, NULL);
renew_utg(ug, read_g, new_rtg_edges);
if(asm_opt.purge_level_primary > 0)
if (!(asm_opt.flag & HA_F_BAN_POST_JOIN))
{
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);
rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
min_ovlp, 0, 0, 1, NULL);
renew_utg(ug, read_g, new_rtg_edges);
rescue_contained_reads_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
min_ovlp, 0, 10, 0, 1, NULL, NULL);
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);
}
}
@@ -26107,7 +26110,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
normalize_ma_hit_t_single_side_advance(sources, n_read);
normalize_ma_hit_t_single_side_advance(reverse_sources, n_read);
// debug_info_of_specfic_read(">m64011_190830_220126/117834372/ccs", sources, reverse_sources,
// debug_info_of_specfic_read("m64062_190803_042216/122882911/ccs", sources, reverse_sources,
// -1, "clean");
@@ -26369,13 +26372,17 @@ long long bubble_dist, int read_graph, int write)
&R_INF, output_file_name);
}
try_rescue_overlaps(sources, reverse_sources, n_read, 4);
if (!(asm_opt.flag & HA_F_BAN_ASSEMBLY))
{
try_rescue_overlaps(sources, reverse_sources, n_read, 4);
clean_graph(min_dp, sources, reverse_sources, n_read, readLen, mini_overlap_length,
max_hang_length, clean_round, gap_fuzz, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
output_file_name, bubble_dist, read_graph, &ruIndex, &sg, &coverage_cut, 0);
asg_destroy(sg);
free(coverage_cut);
}
clean_graph(min_dp, sources, reverse_sources, n_read, readLen, mini_overlap_length,
max_hang_length, clean_round, gap_fuzz, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
output_file_name, bubble_dist, read_graph, &ruIndex, &sg, &coverage_cut, 0);
asg_destroy(sg);
free(coverage_cut);
destory_R_to_U(&ruIndex);
}