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unclean graph

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This commit is contained in:
Haoyu Cheng
2019-11-22 21:58:56 -05:00
parent 2a8e0dc254
commit cb26e0ecd4
1 changed files with 9 additions and 2 deletions
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Overlaps.cpp
+8 -1
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@@ -7825,7 +7825,7 @@ static uint64_t asg_bub_pop1(asg_t *g, uint32_t v0, int max_dist, buf_t *b)
} while (b->S.n > 1 || n_pending); } while (b->S.n > 1 || n_pending);
asg_bub_backtrack(g, v0, b); asg_bub_backtrack(g, v0, b);
n_pop = 1 | (uint64_t)b->T.n<<32; n_pop = 1 | (uint64_t)b->T.n<<32;
fprintf(stderr, "v>>1: %u\n", v0>>1); ///fprintf(stderr, "v>>1: %u\n", v0>>1);
pop_reset: pop_reset:
for (i = 0; i < b->b.n; ++i) { // clear the states of visited vertices for (i = 0; i < b->b.n; ++i) { // clear the states of visited vertices
binfo_t *t = &b->a[b->b.a[i]]; binfo_t *t = &b->a[b->b.a[i]];
@@ -8181,6 +8181,11 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
// debug_info_of_specfic_node("m64016_190918_162737/72220752/ccs", sg, "del_trans"); // debug_info_of_specfic_node("m64016_190918_162737/72220752/ccs", sg, "del_trans");
char* unlean_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(unlean_name, "%s.unclean", output_file_name);
output_read_graph(sg, coverage_cut, unlean_name, n_read);
free(unlean_name);
asg_cut_tip(sg, MAX_SHORT_TIPS); asg_cut_tip(sg, MAX_SHORT_TIPS);
@@ -8276,9 +8281,11 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
asg_cut_tip(sg, MAX_SHORT_TIPS); asg_cut_tip(sg, MAX_SHORT_TIPS);
/****************************may have bugs********************************/ /****************************may have bugs********************************/
asg_arc_del_non_different_haps(sg, reverse_sources, drop_ratio); asg_arc_del_non_different_haps(sg, reverse_sources, drop_ratio);
asg_cut_tip(sg, MAX_SHORT_TIPS); asg_cut_tip(sg, MAX_SHORT_TIPS);
//asg_arc_identify_simple_bubbles(sg); //asg_arc_identify_simple_bubbles(sg);
asg_arc_identify_simple_bubbles_multi(sg, 1); asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_del_short_diploid_by_length(sg, drop_ratio, MAX_SHORT_TIPS); asg_arc_del_short_diploid_by_length(sg, drop_ratio, MAX_SHORT_TIPS);