xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-24 19:38:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

phasing

Browse Source
This commit is contained in:
chhylp123
2020-12-28 03:35:17 -05:00
parent 53a655d802
commit 5d506e82c9
3 changed files with 585 additions and 87 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Overlaps.cpp
+60 -29
View File
@@ -11970,6 +11970,7 @@ kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp)
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, 0, 0, 0, 1, NULL);
dip_thres = ((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE)*0.75;
asm_opt.hom_global_coverage = tmp_cov;
for (i = 0; i < ug->g->n_seq; i++)
{
@@ -12026,52 +12027,48 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
{
kvec_asg_arc_t_warp new_rtg_edges;
kv_init(new_rtg_edges.a);
ma_ug_t *ug = NULL, *copy = NULL;
ma_ug_t *ug = NULL;
ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
hc_links link;
init_hc_links(&link, ug->g->n_seq, R_INF.total_reads);
copy = copy_untig_graph(ug);
asg_t *copy_sg = copy_read_graph(sg);
ma_ug_t *copy_ug = copy_untig_graph(ug);
asm_opt.purge_overlap_len = asm_opt.purge_overlap_len_hic;
asm_opt.purge_simi_rate = asm_opt.purge_simi_rate_hic;
adjust_utg_by_primary(&copy, sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
bubble_dist, tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
max_hang, min_ovlp, &new_rtg_edges, &link);
ma_ug_destroy(copy);
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
new_rtg_edges.a.n = 0;
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp);
/**
fprintf(stderr, "Writing raw unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.r_utg.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "utg", output_file);
fclose(output_file);
sprintf(gfa_name, "%s.r_utg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "utg", output_file);
fclose(output_file);
if(asm_opt.bed_inconsist_rate != 0)
{
sprintf(gfa_name, "%s.r_utg.lowQ.bed", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges,
max_hang, min_ovlp, asm_opt.bed_inconsist_rate, "utg", output_file);
fclose(output_file);
}
free(gfa_name);
**/
classify_untigs(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, &new_rtg_edges,
max_hang, min_ovlp);
hic_analysis(ug, sg, &link);
destory_hc_links(&link);
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_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);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources,
reverse_sources, bubble_dist, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0);
}
ma_ug_t* merge_utg(ma_ug_t **dest, ma_ug_t **src)
@@ -13811,6 +13808,41 @@ ma_ug_t* copy_untig_graph(ma_ug_t *src)
return ug;
}
asg_t* copy_read_graph(asg_t *src)
{
asg_t *dest = NULL;
dest = asg_init();
dest->r_seq = src->r_seq;
dest->m_seq = dest->n_seq = src->n_seq;
dest->seq = (asg_seq_t*)malloc(dest->n_seq * sizeof(asg_seq_t));
memcpy(dest->seq, src->seq, sizeof(asg_seq_t)*dest->n_seq);
dest->m_arc = dest->n_arc = src->n_arc;
dest->arc = (asg_arc_t*)malloc(dest->n_arc*sizeof(asg_arc_t));
memcpy(dest->arc, src->arc, sizeof(asg_arc_t)*dest->n_arc);
dest->is_srt = src->is_srt;
dest->is_symm = src->is_symm;
dest->idx = (uint64_t*)malloc(dest->n_seq*2*8);
memcpy(dest->idx, src->idx, dest->n_seq*2*8);
asg_cleanup(dest);
if(src->seq_vis)
{
dest->seq_vis = (uint8_t*)malloc(dest->n_seq*2*sizeof(uint8_t));
memcpy(dest->seq_vis, src->seq_vis, dest->n_seq*2*sizeof(uint8_t));
}
if(src->n_F_seq > 0 && src->F_seq)
{
dest->n_F_seq = src->n_F_seq;
dest->F_seq = (ma_utg_t*)malloc(dest->n_F_seq*sizeof(ma_utg_t));
memcpy(dest->F_seq, src->F_seq, dest->n_F_seq*sizeof(ma_utg_t));
}
return dest;
}
void clean_trio_untig_graph(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, long long bubble_dist,
long long tipsLen, float tip_drop_ratio, long long stops_threshold,
@@ -28063,8 +28095,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
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,
(asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 0.05, 0.9, max_hang_length,
mini_overlap_length);
(asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length);
free(buf);
}
else