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debug hic_hits

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chhylp123
2021-02-09 18:40:49 -05:00
parent 8467d58ef1
commit 5bb22f701c
3 changed files with 14 additions and 27 deletions
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17
Overlaps.cpp
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@@ -10757,7 +10757,7 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a);
///output_unitig_graph(sg, coverage_cut, output_file_name, sources, ruIndex, max_hang, min_ovlp);
output_unitig_graph(sg, coverage_cut, output_file_name, sources, ruIndex, max_hang, min_ovlp);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources,
reverse_sources, bubble_dist, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0);
@@ -26089,13 +26089,11 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
/*******************************for debug***************************************/
}
rescue_bubble_by_chain(sg, coverage_cut, sources, reverse_sources, bubble_dist,
(asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, 10, gap_fuzz);
if (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))
{
rescue_bubble_by_chain(sg, coverage_cut, sources, reverse_sources, bubble_dist,
(asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, 10, gap_fuzz);
char *buf = (char*)calloc(strlen(output_file_name) + 25, 1);
sprintf(buf, "%s.hic.bench", output_file_name);
benchmark_hic_graph(sg, coverage_cut, buf, sources, reverse_sources, bubble_dist,
@@ -26104,9 +26102,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
}
else if (ha_opt_triobin(&asm_opt))
{
rescue_bubble_by_chain(sg, coverage_cut, sources, reverse_sources, bubble_dist,
(asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, 10, gap_fuzz);
char *buf = (char*)calloc(strlen(output_file_name) + 25, 1);
sprintf(buf, "%s.dip", output_file_name);
output_unitig_graph(sg, coverage_cut, buf, sources, ruIndex, max_hang_length, mini_overlap_length);
@@ -26121,9 +26116,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
}
else if(ha_opt_hic(&asm_opt))
{
rescue_bubble_by_chain(sg, coverage_cut, sources, reverse_sources, bubble_dist,
(asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, 10, gap_fuzz);
char *buf = (char*)calloc(strlen(output_file_name) + 25, 1);
sprintf(buf, "%s.hic", output_file_name);
output_hic_graph(sg, coverage_cut, buf, sources, reverse_sources, bubble_dist,
@@ -26139,9 +26131,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
output_read_graph(sg, coverage_cut, output_file_name, n_read);
}
rescue_bubble_by_chain(sg, coverage_cut, sources, reverse_sources, bubble_dist,
(asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, 10, gap_fuzz);
output_contig_graph_primary_pre(sg, coverage_cut, output_file_name, sources, reverse_sources,
asm_opt.small_pop_bubble_size, asm_opt.max_short_tip, ruIndex, max_hang_length, mini_overlap_length);