xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-01 16:18:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge branch 'chain-tune' into merge2

Browse Source
This commit is contained in:
Heng Li
2020-04-05 12:07:13 -04:00
parent ac3fcc339a f0c53e9948
commit 5917aa2f36
28 changed files with 2068 additions and 4528 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Overlaps.cpp
+41 -58
View File
@@ -52,7 +52,6 @@ void ma_hit_sort_qns(ma_hit_t *a, long long n)
radix_sort_hit_qns(a, a + n);
}
void sort_kvec_t_u64_warp(kvec_t_u64_warp* u_vecs, uint32_t is_descend)
{
radix_sort_arch64(u_vecs->a.a, u_vecs->a.a + u_vecs->a.n);
@@ -68,7 +67,6 @@ void sort_kvec_t_u64_warp(kvec_t_u64_warp* u_vecs, uint32_t is_descend)
}
}
asg_t *asg_init(void)
{
return (asg_t*)calloc(1, sizeof(asg_t));
@@ -4356,7 +4354,7 @@ uint32_t startNode, uint32_t endNode)
}
else
{
fprintf(stderr, "ERROR\n");
fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
}
if(asg_arc_a(g, N_list[2])[0].v == (N_list[0]^1))
@@ -4369,7 +4367,7 @@ uint32_t startNode, uint32_t endNode)
}
else
{
fprintf(stderr, "ERROR\n");
fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
}
if(N_list[3] != N_list[4])
@@ -4920,12 +4918,10 @@ int asg_arc_del_short_diploid_unclean(asg_t *g, float drop_ratio, ma_hit_t_alloc
uint32_t detect_single_path_with_dels(asg_t *g, uint32_t begNode, uint32_t* endNode, long long* Len, buf_t* b)
{
uint32_t v = begNode, w;
uint32_t kv, kw;
(*Len) = 0;
while (1)
{
(*Len)++;
@@ -5594,6 +5590,7 @@ ma_hit_t_alloc* reverse_sources, long long min_edge_length, R_to_U* ruIndex)
if(flag1 == LOOP || flag2 == LOOP)
{
free(b_0.b.a); free(b_1.b.a);
return -1;
}
@@ -5612,6 +5609,7 @@ ma_hit_t_alloc* reverse_sources, long long min_edge_length, R_to_U* ruIndex)
if(l1 <= min_edge_length || l2 <= min_edge_length)
{
free(b_0.b.a); free(b_1.b.a);
return -1;
}
@@ -9051,7 +9049,7 @@ ma_sub_t *coverage_cut, int max_hang, int min_ovlp)
break;
}
}
if(k == nv) fprintf(stderr, "ERROR\n");
if(k == nv) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
av = asg_arc_a(read_g, v);
nv = asg_arc_n(read_g, v);
@@ -9065,7 +9063,7 @@ ma_sub_t *coverage_cut, int max_hang, int min_ovlp)
}
}
if(k == nv) fprintf(stderr, "ERROR\n");
if(k == nv) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
if(pE->el == 1 && aE->el == 1) continue;
@@ -9146,7 +9144,7 @@ ma_sub_t *coverage_cut, int max_hang, int min_ovlp)
}
l = asg_arc_len(t_f);
}
if(l == (uint32_t)-1) fprintf(stderr, "ERROR\n");
if(l == (uint32_t)-1) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
/*******************************for debug************************************/
@@ -9195,7 +9193,7 @@ ma_sub_t *coverage_cut, int max_hang, int min_ovlp)
}
l = asg_arc_len(t_f);
}
if(l == (uint32_t)-1) fprintf(stderr, "ERROR\n");
if(l == (uint32_t)-1) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
/*******************************for debug************************************/
@@ -11671,7 +11669,7 @@ void print_untig(ma_ug_t *g, uint32_t uId, const char* info, uint32_t is_print_r
for (k = 0; k < u->n; k++)
{
fprintf(stderr, "%s: rId>>1: %lu, dir: %lu, name: %.*s\n",
info, u->a[k]>>33, (u->a[k]>>32)&1,
info, (unsigned long)(u->a[k]>>33), (unsigned long)((u->a[k]>>32)&1),
(int)Get_NAME_LENGTH((R_INF), (u->a[k]>>33)), Get_NAME((R_INF), (u->a[k]>>33)));
}
}
@@ -13640,8 +13638,6 @@ int load_ma_hit_ts(ma_hit_t_alloc** x, char* read_file_name)
}
void write_ma(ma_hit_t* x, FILE* fp)
{
fwrite(&(x->qns), sizeof(x->qns), 1, fp);
@@ -13708,35 +13704,28 @@ All_reads *RNF, char* output_file_name)
free(gfa_name);
}
int load_all_data_from_disk(ma_hit_t_alloc **sources, ma_hit_t_alloc **reverse_sources,
char* output_file_name)
int load_all_data_from_disk(ma_hit_t_alloc **sources, ma_hit_t_alloc **reverse_sources, char* output_file_name)
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.ovlp", output_file_name);
if(!load_All_reads(&R_INF, gfa_name))
{
return 0;
}
sprintf(gfa_name, "%s.ovlp.source", output_file_name);
if(!load_ma_hit_ts(sources, gfa_name))
{
return 0;
}
sprintf(gfa_name, "%s.ovlp.reverse", output_file_name);
if(!load_ma_hit_ts(reverse_sources, gfa_name))
{
return 0;
}
return 1;
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.ovlp", output_file_name);
if (!load_All_reads(&R_INF, gfa_name)) {
free(gfa_name);
return 0;
}
sprintf(gfa_name, "%s.ovlp.source", output_file_name);
if (!load_ma_hit_ts(sources, gfa_name)) {
free(gfa_name);
return 0;
}
sprintf(gfa_name, "%s.ovlp.reverse", output_file_name);
if (!load_ma_hit_ts(reverse_sources, gfa_name)) {
free(gfa_name);
return 0;
}
free(gfa_name);
return 1;
}
// count the number of outgoing arcs, excluding reduced arcs
static inline int count_out(const asg_t *g, uint32_t v)
{
@@ -21006,7 +20995,7 @@ void merge_ug_nodes(ma_ug_t *ug, asg_t* read_g, kvec_t_u64_warp* array)
if(aw[i].del) continue;
if(aw[i].v == (v^1)) break;
}
if(i == nw) fprintf(stderr, "ERROR\n");
if(i == nw) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
kmp = kmp | (uint64_t)(aw[i].ol);
@@ -21037,7 +21026,7 @@ void merge_ug_nodes(ma_ug_t *ug, asg_t* read_g, kvec_t_u64_warp* array)
if(aw[i].del) continue;
if(aw[i].v == (v^1)) break;
}
if(i == nw) fprintf(stderr, "ERROR\n");
if(i == nw) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
kmp = kmp | (uint64_t)(aw[i].ol);
@@ -26198,7 +26187,7 @@ void fix_binned_reads(ma_hit_t_alloc* paf, uint64_t n_read, ma_sub_t* coverage_c
}
fprintf(stderr, "n_read: %lu, binned_reads: %lu, binned_error_reads: %lu\n",
n_read, binned_reads, binned_error_reads);
(unsigned long)n_read, (unsigned long)binned_reads, (unsigned long)binned_error_reads);
}
@@ -26301,24 +26290,22 @@ int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long n_read, uint64_t* readLen, long long mini_overlap_length,
long long max_hang_length, long long clean_round, long long gap_fuzz,
float min_ovlp_drop_ratio, float max_ovlp_drop_ratio, char* output_file_name,
long long bubble_dist, int read_graph, R_to_U* ruIndex, asg_t* sg,
ma_sub_t* coverage_cut, int debug_g)
long long bubble_dist, int read_graph, R_to_U* ruIndex, asg_t **sg_ptr,
ma_sub_t **coverage_cut_ptr, int debug_g)
{
ma_sub_t *coverage_cut = *coverage_cut_ptr;
asg_t *sg = *sg_ptr;
if(debug_g) goto debug_gfa;
///just for debug
renew_graph_init(sources, reverse_sources, sg, coverage_cut, ruIndex, n_read);
///it's hard to say which function is better
///normalize_ma_hit_t_single_side(sources, n_read);
normalize_ma_hit_t_single_side_advance(sources, n_read);
normalize_ma_hit_t_single_side_advance(reverse_sources, n_read);
// debug_info_of_specfic_read(">m64011_190830_220126/117834372/ccs", sources, reverse_sources,
// -1, "clean");
@@ -26532,13 +26519,13 @@ ma_sub_t* coverage_cut, int debug_g)
bubble_dist, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 0.05, 0.9, max_hang_length,
mini_overlap_length);
output_contig_graph_alternative(sg, coverage_cut, output_file_name, sources, max_hang_length, mini_overlap_length);
}
*coverage_cut_ptr = coverage_cut;
*sg_ptr = sg;
}
void build_string_graph_without_clean(
int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long n_read, uint64_t* readLen, long long mini_overlap_length,
@@ -26551,8 +26538,7 @@ long long bubble_dist, int read_graph, int write)
asg_t *sg = NULL;
ma_sub_t* coverage_cut = NULL;
// debug_info_of_specfic_read("m64011_190329_072846/80545633/ccs",
// sources, reverse_sources, -1, "clean");
// debug_info_of_specfic_read("m64011_190329_072846/80545633/ccs", sources, reverse_sources, -1, "clean");
///actually min_thres = asm_opt.max_short_tip + 1 there are asm_opt.max_short_tip reads
min_thres = asm_opt.max_short_tip + 1;
@@ -26565,7 +26551,7 @@ long long bubble_dist, int read_graph, int write)
clean_graph(min_dp, sources, reverse_sources, n_read, readLen, mini_overlap_length,
max_hang_length, clean_round, gap_fuzz, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
output_file_name, bubble_dist, read_graph, &ruIndex, sg, coverage_cut, 1);
output_file_name, bubble_dist, read_graph, &ruIndex, &sg, &coverage_cut, 1);
asg_destroy(sg);
free(coverage_cut);
destory_R_to_U(&ruIndex);
@@ -26573,20 +26559,17 @@ long long bubble_dist, int read_graph, int write)
}
}
if (asm_opt.write_index_to_disk && write)
{
write_all_data_to_disk(sources, reverse_sources,
&R_INF, output_file_name);
}
try_rescue_overlaps(sources, reverse_sources, n_read, 4);
clean_graph(min_dp, sources, reverse_sources, n_read, readLen, mini_overlap_length,
max_hang_length, clean_round, gap_fuzz, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
output_file_name, bubble_dist, read_graph, &ruIndex, sg, coverage_cut, 0);
output_file_name, bubble_dist, read_graph, &ruIndex, &sg, &coverage_cut, 0);
asg_destroy(sg);
free(coverage_cut);