From a8aa37d2010e9885c67a5c619c3cd3c696006085 Mon Sep 17 00:00:00 2001 From: chhylp123 Date: Wed, 5 Aug 2020 17:45:23 -0400 Subject: [PATCH] fix makefile --- Overlaps.cpp | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/Overlaps.cpp b/Overlaps.cpp index 7f5076d..b9b542d 100644 --- a/Overlaps.cpp +++ b/Overlaps.cpp @@ -26841,8 +26841,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g) ///just need to deal with trio here ma_hit_contained_advance(sources, n_read, coverage_cut, ruIndex, max_hang_length, mini_overlap_length); - // debug_info_of_specfic_read("m54329U_190617_231905/176226420/ccs", sources, reverse_sources, - // -1, "clean"); + ///debug_info_of_specfic_read("m54329U_190827_173812/166332272/ccs", sources, reverse_sources, -1, "clean"); sg = ma_sg_gen(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length); asg_arc_del_trans(sg, gap_fuzz); @@ -26859,8 +26858,8 @@ ma_sub_t **coverage_cut_ptr, int debug_g) asg_cut_tip(sg, asm_opt.max_short_tip); ///drop_inexact_edegs_at_bubbles(sg, bubble_dist); - ///debug_info_of_specfic_node("m54329U_190617_231905/176226420/ccs", sg, "complex_false_link"); - + ///debug_info_of_specfic_node("m54329U_190827_173812/166332272/ccs", sg, "beg"); + if(clean_round > 0) { double cut_step; @@ -26886,13 +26885,14 @@ ma_sub_t **coverage_cut_ptr, int debug_g) fprintf(stderr, "\n\n**********%d-th round drop: drop_ratio = %f**********\n", i, drop_ratio); } - + ///just topological clean pre_clean(sources, coverage_cut, sg, bubble_dist); ///asg_arc_del_orthology(sg, reverse_sources, drop_ratio, asm_opt.max_short_tip); // asg_arc_del_orthology_multiple_way(sg, reverse_sources, drop_ratio, asm_opt.max_short_tip); // asg_cut_tip(sg, asm_opt.max_short_tip); /****************************may have bugs********************************/ + asg_arc_identify_simple_bubbles_multi(sg, 1); //reomve edge between two chromesomes //this node must be a single read @@ -26900,6 +26900,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g) asg_cut_tip(sg, asm_opt.max_short_tip); /****************************may have bugs********************************/ /****************************may have bugs********************************/ + ///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); @@ -26913,6 +26914,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g) } asg_cut_tip(sg, asm_opt.max_short_tip); /****************************may have bugs********************************/ + asg_arc_identify_simple_bubbles_multi(sg, 1); if (ha_opt_triobin(&asm_opt)) { @@ -26928,7 +26930,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g) asg_arc_identify_simple_bubbles_multi(sg, 1); asg_arc_del_short_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, - asm_opt.max_short_tip, ruIndex); + asm_opt.max_short_tip, ruIndex); asg_arc_identify_simple_bubbles_multi(sg, 1); asg_arc_del_complex_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, asm_opt.max_short_tip);