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fix makefile

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chhylp123
2020-08-05 17:45:23 -04:00
parent 320dc58127
commit a8aa37d201
1 changed files with 8 additions and 6 deletions
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Overlaps.cpp
+8 -6
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@@ -26841,8 +26841,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///just need to deal with trio here ///just need to deal with trio here
ma_hit_contained_advance(sources, n_read, coverage_cut, ruIndex, max_hang_length, mini_overlap_length); 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, ///debug_info_of_specfic_read("m54329U_190827_173812/166332272/ccs", sources, reverse_sources, -1, "clean");
// -1, "clean");
sg = ma_sg_gen(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length); sg = ma_sg_gen(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
asg_arc_del_trans(sg, gap_fuzz); 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); asg_cut_tip(sg, asm_opt.max_short_tip);
///drop_inexact_edegs_at_bubbles(sg, bubble_dist); ///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) if(clean_round > 0)
{ {
double cut_step; 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", fprintf(stderr, "\n\n**********%d-th round drop: drop_ratio = %f**********\n",
i, drop_ratio); i, drop_ratio);
} }
///just topological clean ///just topological clean
pre_clean(sources, coverage_cut, sg, bubble_dist); 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(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_arc_del_orthology_multiple_way(sg, reverse_sources, drop_ratio, asm_opt.max_short_tip);
// asg_cut_tip(sg, asm_opt.max_short_tip); // 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, 1);
//reomve edge between two chromesomes //reomve edge between two chromesomes
//this node must be a single read //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); asg_cut_tip(sg, asm_opt.max_short_tip);
/****************************may have bugs********************************/ /****************************may have bugs********************************/
/****************************may have bugs********************************/ /****************************may have bugs********************************/
///asg_arc_identify_simple_bubbles_multi(sg, 1); ///asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_identify_simple_bubbles_multi(sg, 0); asg_arc_identify_simple_bubbles_multi(sg, 0);
///asg_arc_del_short_diploid_unclean_exact(sg, drop_ratio, sources); ///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); 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, 1);
if (ha_opt_triobin(&asm_opt)) 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_identify_simple_bubbles_multi(sg, 1);
asg_arc_del_short_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, 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_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); asg_arc_del_complex_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, asm_opt.max_short_tip);