xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-25 02:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

debug ul

Browse Source
This commit is contained in:
chhylp123
2021-10-10 13:37:32 -04:00
parent 7dd4a848b9
commit cb320b88f3
7 changed files with 1212 additions and 325 deletions
Download Patch File Download Diff File Expand all files Collapse all files
htab.cpp
+129 -2
View File
@@ -509,8 +509,7 @@ void ha_pt_destroy(ha_pt_t *h)
}
if(h->h[i].al){
free(h->h[i].al); h->h[i].al = NULL;
}
}
}
free(h->h); free(h);
}
@@ -634,6 +633,7 @@ int sf##_ha_pt_insert_list(ha_pt_t *h, int n, const HType *a)\
ha_pt1_t *g;\
if (n == 0) return 0;\
g = &h->h[a[0].x&mask];\
/**fprintf(stderr, "a[0].x&mask: %lu, a[0].x&mask: %lu, n: %d\n", a[0].x&mask, a[0].x, n);**/\
for (j = 0; j < n; ++j) {\
uint64_t x = a[j].x >> h->pre;\
khint_t k;\
@@ -643,6 +643,7 @@ int sf##_ha_pt_insert_list(ha_pt_t *h, int n, const HType *a)\
k = yak_pt_get(g->h, x<<YAK_COUNTER_BITS);\
if (k == kh_end(g->h)) continue; \
n = kh_key(g->h, k) & YAK_MAX_COUNT;\
/**fprintf(stderr, "j: %d, n: %d\n", j, n);**/\
assert(n < YAK_MAX_COUNT);\
p = &g->Ia[kh_val(g->h, k) + n];\
p->rid = a[j].rid, p->rev = a[j].rev, p->pos = a[j].pos, p->span = a[j].span;\
@@ -973,6 +974,7 @@ ha_ct_t *ha_count(const hifiasm_opt_t *asm_o, int flag, int HPC, int k, int w, h
///for ha_pt_gen, shoud be 0
opt.bf_shift = flag & HAF_COUNT_EXACT? 0 : asm_o->bf_shift;
opt.n_thread = asm_o->thread_num;
// opt.n_thread = p0? 1: asm_o->thread_num;
opt.adaLen = (keep_adapter? asm_o->adapterLen : 0);
opt.min_rcnt = (low_freq?*low_freq:-1);
///asm_opt->num_reads is the number of fastq files
@@ -1083,11 +1085,15 @@ ha_pt_t *ha_pt_ug_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, ma_utg_
ct = ha_count(asm_opt, HAF_COUNT_EXACT|HAF_UG_READ, is_HPC, k, w, NULL, flt_tab, NULL, us, 0, NULL);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> counted %ld distinct minimizer k-mers\n", __func__,
yak_realtime(), yak_cpu_usage(), (long)ct->tot);
exit(1);
///minimizer with YAK_MAX_COUNT occ may apper > YAK_MAX_COUNT times, so it may lead to overflow at ha_pt_gen
ha_ct_shrink(ct, min_freq, YAK_MAX_COUNT - 1, asm_opt->thread_num);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> sb0\n", __func__, yak_realtime(), yak_cpu_usage());
pt = ha_pt_gen(ct, asm_opt->thread_num, 1);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> sb1\n", __func__, yak_realtime(), yak_cpu_usage());
ha_count(asm_opt, HAF_COUNT_EXACT|HAF_UG_READ, is_HPC, k, w, pt, flt_tab, NULL, us, 0, NULL);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> sb2\n", __func__, yak_realtime(), yak_cpu_usage());
//ha_pt_sort(pt, asm_opt->thread_num);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> indexed %ld positions\n", __func__,
yak_realtime(), yak_cpu_usage(), (long)pt->tot_pos);
@@ -1436,3 +1442,124 @@ int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads* r, hifiasm_op
free(gfa_name);
return 1;
}
int uidx_write(void *flt_tab, ha_pt_t *ha_idx, char* file_name)
{
char* gfa_name = (char*)malloc(strlen(file_name)+25);
sprintf(gfa_name, "%s.uidx.bin", file_name);
FILE* fp = fopen(gfa_name, "w");
if (!fp) {
free(gfa_name);
return 0;
}
yak_ft_t *ha_flt_tab = (yak_ft_t*)flt_tab;
if(ha_flt_tab)
{
fwrite("f", 1, 1, fp);
yak_ft_save(ha_flt_tab, fp);
}
if(ha_idx)
{
int i;
ha_pt1_t *g;
fwrite("h", 1, 1, fp);
fwrite(&ha_idx->k, sizeof(ha_idx->k), 1, fp);
fwrite(&ha_idx->pre, sizeof(ha_idx->pre), 1, fp);
fwrite(&ha_idx->tot, sizeof(ha_idx->tot), 1, fp);
fwrite(&ha_idx->tot_pos, sizeof(ha_idx->tot_pos), 1, fp);
for (i = 0; i < 1<<ha_idx->pre; ++i)
{
g = &(ha_idx->h[i]);
yak_pt_save(g->h, fp);
fwrite(&g->n, sizeof(g->n), 1, fp);
fwrite(g->al, sizeof(ha_idxposl_t), g->n, fp);
}
}
fprintf(stderr, "[M::%s] Index has been written.\n", __func__);
free(gfa_name);
fclose(fp);
return 1;
}
int uidx_load(void **r_flt_tab, ha_pt_t **r_ha_idx, char* file_name)
{
char* gfa_name = (char*)malloc(strlen(file_name)+25);
sprintf(gfa_name, "%s.uidx.bin", file_name);
FILE* fp = fopen(gfa_name, "r");
if (!fp) {
free(gfa_name);
return 0;
}
ha_pt_t *ha_idx = NULL;
char mode = 0;
int f_flag = 0, i;
double index_time, index_s_time, pos_time, pos_s_time;
f_flag += fread(&mode, 1, 1, fp);
if(mode == 'f')
{
index_time = yak_realtime();
yak_ft_load((yak_ft_t **)r_flt_tab, fp);
f_flag += fread(&mode, 1, 1, fp);
fprintf(stderr, "[M::%s::%.3f] ==> Loaded flt table\n", __func__, yak_realtime()-index_time);
}
///insert using multiple threads???
if(mode == 'h')
{
pos_time = index_time = 0;
CALLOC(ha_idx, 1);
ha_pt1_t *g;
f_flag += fread(&ha_idx->k, sizeof(ha_idx->k), 1, fp);
f_flag += fread(&ha_idx->pre, sizeof(ha_idx->pre), 1, fp);
f_flag += fread(&ha_idx->tot, sizeof(ha_idx->tot), 1, fp);
f_flag += fread(&ha_idx->tot_pos, sizeof(ha_idx->tot_pos), 1, fp);
CALLOC(ha_idx->h, 1<<ha_idx->pre);
for (i = 0; i < 1<<ha_idx->pre; ++i)
{
index_s_time = yak_realtime();
g = &(ha_idx->h[i]);
yak_pt_load(&(g->h), fp);
index_time += yak_realtime() - index_s_time;
pos_s_time = yak_realtime();
f_flag += fread(&g->n, sizeof(g->n), 1, fp);
MALLOC(g->al, g->n);
f_flag += fread(g->al, sizeof(ha_idxposl_t), g->n, fp);
pos_time += yak_realtime() - pos_s_time;
}
(*r_ha_idx) = ha_idx;
fprintf(stderr, "[M::%s::%.3f(index)/%.3f(pos)] ==> Loaded pos table\n", __func__, index_time, pos_time);
}
if(mode != 'h' && mode != 'f')
{
free(gfa_name);
fclose(fp);
return 0;
}
fprintf(stderr, "[M::%s] Index has been loaded.\n", __func__);
fclose(fp);
free(gfa_name);
return 1;
}