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backup phasing

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chhylp123
2021-05-31 04:19:05 -04:00
parent e774a83be2
commit aa164949f2
5 changed files with 71 additions and 55 deletions
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Overlaps.cpp
+15 -16
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@@ -12837,7 +12837,7 @@ void set_r_het_flag(ma_ug_t *ug, asg_t *sg, ma_sub_t* coverage_cut, ma_hit_t_all
// dip_thre_max *= 0.75;
dip_thre_max = (double)(dip_thre_max) - (((double)(dip_thre_max)*0.5)/asm_opt.polyploidy);
fprintf(stderr, "dip_thre_max: %lu\n", dip_thre_max);
// fprintf(stderr, "dip_thre_max: %lu\n", dip_thre_max);
for (m = 0; m < ug->g->n_seq; m++)
{
@@ -13069,7 +13069,7 @@ void write_trans_chain(trans_chain* t_ch, const char *fn)
}
trans_chain* load_hc_hits(const char *fn)
trans_chain* load_hc_trans(const char *fn)
{
uint64_t flag = 0;
char *buf = (char*)calloc(strlen(fn) + 25, 1);
@@ -13148,7 +13148,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
hap_cov_t *cov = NULL;
trans_chain* t_ch = NULL;
if((asm_opt.flag & HA_F_VERBOSE_GFA)) t_ch = load_hc_hits(output_file_name);
if((asm_opt.flag & HA_F_VERBOSE_GFA)) t_ch = load_hc_trans(output_file_name);
if(!t_ch)
{
@@ -13308,7 +13308,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
fclose(output_file);
free(gfa_name);
if((asm_opt.flag & HA_F_VERBOSE_GFA)) t_ch = load_hc_hits(output_file_name);
if((asm_opt.flag & HA_F_VERBOSE_GFA)) t_ch = load_hc_trans(output_file_name);
if(!t_ch)
{
t_ch = get_hic_polyploid_trans_chain(ug, sg, coverage_cut, sources, reverse_sources, max_hang, min_ovlp, ruIndex, b_mask_t);
@@ -13317,7 +13317,7 @@ long long gap_fuzz, bub_label_t* b_mask_t)
if((asm_opt.flag & HA_F_VERBOSE_GFA)) write_trans_chain(t_ch, output_file_name);
}
hic_analysis(ug, sg, t_ch, &opt, 1);
hic_analysis(ug, sg, t_ch, &opt, 0);
destory_trans_chain(&t_ch);
ma_ug_destroy(ug);
asg_cleanup(sg);
@@ -14101,7 +14101,6 @@ long long tipsLen, float tip_drop_ratio, long long stops_threshold,
R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp,
bub_label_t* b_mask_t)
{
fprintf(stderr, "******0******\n");
kvec_asg_arc_t_warp new_rtg_edges;
kv_init(new_rtg_edges.a);
ma_ug_t *ug = NULL;
@@ -14112,13 +14111,13 @@ bub_label_t* b_mask_t)
asg_t *copy_sg = copy_read_graph(sg);
ma_ug_t *copy_ug = copy_untig_graph(ug);
/*******************************for debug************************************/
// adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
// tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
// max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1, 1);
adjust_utg_advance(copy_sg, copy_ug, reverse_sources, ruIndex, b_mask_t);
get_utg_ovlp(&copy_ug, copy_sg, sources, reverse_sources, coverage_cut,
ruIndex, max_hang, min_ovlp, &new_rtg_edges, b_mask_t, NULL);
exit(1);
adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1, 1);
// adjust_utg_advance(copy_sg, copy_ug, reverse_sources, ruIndex, b_mask_t);
// get_utg_ovlp(&copy_ug, copy_sg, sources, reverse_sources, coverage_cut,
// ruIndex, max_hang, min_ovlp, &new_rtg_edges, b_mask_t, NULL);
// exit(1);
/*******************************for debug************************************/
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
@@ -30816,10 +30815,10 @@ 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, gap_fuzz, &b_mask_t);
output_hic_graph_polyploid(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2),
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, gap_fuzz, &b_mask_t);
// output_hic_graph_polyploid(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, gap_fuzz, &b_mask_t);
}
else if((asm_opt.flag & HA_F_PARTITION) && (asm_opt.purge_level_primary > 0))
{