From cb26e0ecd45b2a88d1c14694de5a5e10e94b7137 Mon Sep 17 00:00:00 2001 From: Haoyu Cheng Date: Fri, 22 Nov 2019 21:58:56 -0500 Subject: [PATCH] unclean graph --- Overlaps.cpp | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/Overlaps.cpp b/Overlaps.cpp index 3aaf903..7a9c6ea 100644 --- a/Overlaps.cpp +++ b/Overlaps.cpp @@ -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); asg_bub_backtrack(g, v0, b); 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: for (i = 0; i < b->b.n; ++i) { // clear the states of visited vertices 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"); + 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); @@ -8276,8 +8281,10 @@ char* output_file_name, long long bubble_dist, int read_graph, int write) asg_cut_tip(sg, MAX_SHORT_TIPS); /****************************may have bugs********************************/ + asg_arc_del_non_different_haps(sg, reverse_sources, drop_ratio); asg_cut_tip(sg, MAX_SHORT_TIPS); + //asg_arc_identify_simple_bubbles(sg); asg_arc_identify_simple_bubbles_multi(sg, 1); @@ -8341,7 +8348,7 @@ char* output_file_name, long long bubble_dist, int read_graph, int write) asg_arc_identify_simple_bubbles_multi(sg, 0); asg_arc_del_too_short_overlaps(sg, 2000, min_ovlp_drop_ratio, reverse_sources); asg_cut_tip(sg, MAX_SHORT_TIPS); - +