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bug fixing for purge_dup

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chhylp123
2020-04-08 16:55:04 -04:00
parent 9cc563c7c6
commit a288415111
4 changed files with 175 additions and 66 deletions
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Overlaps.cpp
+6 -6
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@@ -22194,6 +22194,8 @@ char* output_file_name, ma_hit_t_alloc** reverse_sources, R_to_U* ruIndex)
return 0;
}
R_INF.paf = (*sources); R_INF.reverse_paf = (*reverse_sources);
return 1;
}
@@ -22276,7 +22278,8 @@ kvec_asg_arc_t_warp* 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);
@@ -22286,28 +22289,25 @@ kvec_asg_arc_t_warp* 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);
///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();
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);
///set_drop_trio_flag(*ug);
n_vtx = read_g->n_seq;
for (v = 0; v < n_vtx; v++)