xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-25 20:48:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

for debugging

Browse Source
This commit is contained in:
chhylp123
2020-10-11 14:32:33 -04:00
parent 7a314d1ef3
commit 89fcb35a64
9 changed files with 192 additions and 41 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Overlaps.cpp
+25 -9
View File
@@ -2107,20 +2107,30 @@ static inline int asg_is_single_edge(const asg_t *g, uint32_t v, uint32_t start_
return nv;
}
void debug_info_of_specfic_node(const char* name, asg_t *g, char* command)
void debug_info_of_specfic_node(char* name, asg_t *g, R_to_U* ruIndex, char* command)
{
fprintf(stderr, "\n\n\n");
uint32_t v, n_vtx = g->n_seq * 2, queryLen = strlen(name), flag = 0;
uint32_t v, n_vtx = g->n_seq * 2, queryLen = strlen(name), flag = 0, contain_rId, is_Unitig;
for (v = 0; v < n_vtx; ++v)
{
if(queryLen == Get_NAME_LENGTH(R_INF, (v>>1)) && memcmp(name, Get_NAME(R_INF, (v>>1)), Get_NAME_LENGTH(R_INF, (v>>1))) == 0)
{
if(flag == 0) fprintf(stderr, "\nafter %s\n", command);
fprintf(stderr, "****************graph ref_read: %.*s, dir: %u****************\n",
(int)Get_NAME_LENGTH(R_INF, (v>>1)), Get_NAME(R_INF, (v>>1)), v&1);
fprintf(stderr, "****************graph ref_read: %.*s, id: %u, dir: %u****************\n",
(int)Get_NAME_LENGTH(R_INF, (v>>1)), Get_NAME(R_INF, (v>>1)), v>>1, v&1);
if(g->seq[v>>1].del)
{
fprintf(stderr, "read has already been deleted.\n");
get_R_to_U(ruIndex, (v>>1), &contain_rId, &is_Unitig);
if(contain_rId != (uint32_t)-1 && is_Unitig != 1)
{
fprintf(stderr, "read is deleted as a contained read by: %.*s\n contain_rId: %u, del: %u\n",
(int)Get_NAME_LENGTH(R_INF, contain_rId), Get_NAME(R_INF, contain_rId), contain_rId, g->seq[contain_rId].del);
}
else
{
fprintf(stderr, "read has already been deleted.\n");
}
return;
}
@@ -9757,12 +9767,13 @@ ma_hit_t_alloc* reverse_sources, int id, const char* command)
for (j = 0; j < reverse_sources[i].length; j++)
{
tn = Get_tn(reverse_sources[i].buffer[j]);
fprintf(stderr, "target: %.*s, qs: %u, qe: %u, ts: %u, te: %u, del: %u\n",
fprintf(stderr, "target: %.*s, qs: %u, qe: %u, ts: %u, te: %u, rev: %u, del: %u\n",
(int)Get_NAME_LENGTH(R_INF, tn), Get_NAME(R_INF, tn),
Get_qs(reverse_sources[i].buffer[j]),
Get_qe(reverse_sources[i].buffer[j]),
Get_ts(reverse_sources[i].buffer[j]),
Get_te(reverse_sources[i].buffer[j]),
reverse_sources[i].buffer[j].rev,
(uint32_t)sources[i].buffer[j].del);
}
@@ -26919,6 +26930,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///it seems we do not need ma_hit_cut & ma_hit_flt
ma_hit_sub(min_dp, sources, n_read, readLen, mini_overlap_length, &coverage_cut);
detect_chimeric_reads(sources, n_read, readLen, coverage_cut, asm_opt.max_ov_diff_final * 2.0);
ma_hit_cut(sources, n_read, readLen, mini_overlap_length, &coverage_cut);
///print_binned_reads(sources, n_read, coverage_cut);
ma_hit_flt(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
@@ -26926,8 +26938,10 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///fix_binned_reads(sources, n_read, coverage_cut);
///just need to deal with trio here
ma_hit_contained_advance(sources, n_read, coverage_cut, ruIndex, max_hang_length, mini_overlap_length);
sg = ma_sg_gen(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
///debug_info_of_specfic_node((char*)"m64062_190804_172951/130483063/ccs", sg, ruIndex, (char*)"sbsbsb");
asg_arc_del_trans(sg, gap_fuzz);
asm_opt.coverage = get_coverage(sources, coverage_cut, n_read);
@@ -27154,9 +27168,11 @@ long long bubble_dist, int read_graph, int write)
&R_INF, output_file_name);
}
debug_info_of_specfic_read("m64062_190803_042216/120916077/ccs", sources, reverse_sources, -1, "beg");
debug_info_of_specfic_read("m64062_190806_063919/71436446/ccs", sources, reverse_sources, -1, "beg");
debug_info_of_specfic_read("m64062_190803_042216/82117654/ccs", sources, reverse_sources, -1, "beg");
///debug_info_of_specfic_read("m64062_190803_042216/15205346/ccs", sources, reverse_sources, -1, "beg");
if (!(asm_opt.flag & HA_F_BAN_ASSEMBLY))
{
try_rescue_overlaps(sources, reverse_sources, n_read, 4);