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bug fixing

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chhylp123
2021-04-16 22:26:28 -04:00
parent f8ee584291
commit efacf8e796
5 changed files with 68 additions and 1070 deletions
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Overlaps.cpp
+9 -3
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@@ -12603,7 +12603,9 @@ bub_label_t* b_mask_t)
hap_cov_t *cov = NULL;
trans_chain* t_ch = load_hc_hits(output_file_name);
trans_chain* t_ch = NULL;
if((asm_opt.flag & HA_F_VERBOSE_GFA)) t_ch = load_hc_hits(output_file_name);
if(!t_ch)
{
new_rtg_edges.a.n = 0;
@@ -12627,7 +12629,7 @@ bub_label_t* b_mask_t)
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges,
max_hang, min_ovlp, asm_opt.hic_inconsist_rate, NULL, NULL, cov);
write_trans_chain(cov->t_ch, output_file_name);
if((asm_opt.flag & HA_F_VERBOSE_GFA)) write_trans_chain(cov->t_ch, output_file_name);
}
hic_analysis(ug, sg, cov?cov->t_ch:t_ch);
@@ -30000,11 +30002,13 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
if (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))
{
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;
benchmark_hic_graph(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3,
ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, &b_mask_t);
}
else if (ha_opt_triobin(&asm_opt))
{
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;
output_trio_unitig_graph(sg, coverage_cut, o_file, FATHER, sources,
reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t);
@@ -30014,16 +30018,18 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
}
else if(ha_opt_hic(&asm_opt))
{
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;
output_hic_graph(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2),
0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, &b_mask_t);
}
else if(asm_opt.flag & HA_F_PARTITION)
else if((asm_opt.flag & HA_F_PARTITION) && (asm_opt.purge_level_primary > 0))
{
output_bp_graph(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2),
0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, &b_mask_t);
}
else
{
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;
output_contig_graph_primary(sg, coverage_cut, o_file, sources, reverse_sources,
(asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, &b_mask_t);