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unsucessful hpc mark

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chhylp123
2026-05-15 19:02:16 -04:00
parent 7884b5ad88
commit bca2394b69
12 changed files with 2679 additions and 216 deletions
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htab.cpp
+41 -7
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@@ -1420,7 +1420,7 @@ int load_ct_index(void **i_ct_idx, char* file_name)
return 1;
}
int write_pt_index(void *flt_tab, ha_pt_t *ha_idx, All_reads* r, hifiasm_opt_t* opt, char* file_name)
int write_pt_index(void *flt_tab, ha_pt_t *ha_idx, All_reads* r, hifiasm_opt_t* opt, char* file_name, uint8_t force_rpaf_load)
{
char* gfa_name = (char*)malloc(strlen(file_name)+64);
if(r) sprintf(gfa_name, "%s.pt_flt", file_name);
@@ -1479,6 +1479,19 @@ int write_pt_index(void *flt_tab, ha_pt_t *ha_idx, All_reads* r, hifiasm_opt_t*
fwrite(&(r->paf[k].length), sizeof(r->paf[k].length), 1, fp);
fwrite(r->paf[k].buffer, sizeof((*(r->paf[k].buffer))), r->paf[k].length, fp);
}
int8_t rff = opt->post_syn;
if(force_rpaf_load) rff = 1;
fwrite(&rff, sizeof(rff), 1, fp);
if(rff) {
for (k = 0; k < r->total_reads; k++) {
fwrite(&(r->reverse_paf[k].is_fully_corrected), sizeof(r->reverse_paf[k].is_fully_corrected), 1, fp);
fwrite(&(r->reverse_paf[k].is_abnormal), sizeof(r->reverse_paf[k].is_abnormal), 1, fp);
fwrite(&(r->reverse_paf[k].length), sizeof(r->reverse_paf[k].length), 1, fp);
fwrite(r->reverse_paf[k].buffer, sizeof((*(r->reverse_paf[k].buffer))), r->reverse_paf[k].length, fp);
}
}
}
fprintf(stderr, "[M::%s] Index has been written.\n", __func__);
@@ -1487,7 +1500,7 @@ int write_pt_index(void *flt_tab, ha_pt_t *ha_idx, All_reads* r, hifiasm_opt_t*
return 1;
}
int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads *r, hifiasm_opt_t* opt, char* file_name)
int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads *r, hifiasm_opt_t* opt, char* file_name, uint8_t force_rpaf_load)
{
char* gfa_name = (char*)malloc(strlen(file_name)+64);
if(r) sprintf(gfa_name, "%s.pt_flt", file_name);
@@ -1604,6 +1617,27 @@ int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads *r, hifiasm_op
r->paf[k].buffer = (ma_hit_t*)malloc(sizeof(ma_hit_t)*r->paf[k].length);
fread(r->paf[k].buffer, sizeof((*(r->paf[k].buffer))), r->paf[k].length, fp);
}
int8_t rff = 0;
f_flag += fread(&rff, sizeof(rff), 1, fp);
if(!force_rpaf_load) {
opt->post_syn = rff;
fprintf(stderr, "[M::%s] overwritten post_syn to::%u\n", __func__, (uint32_t)opt->post_syn);
}
if(rff) {
for (k = 0; k < r->total_reads; k++) {
f_flag += fread(&(r->reverse_paf[k].is_fully_corrected), sizeof(r->reverse_paf[k].is_fully_corrected), 1, fp);
f_flag += fread(&(r->reverse_paf[k].is_abnormal), sizeof(r->reverse_paf[k].is_abnormal), 1, fp);
f_flag += fread(&(r->reverse_paf[k].length), sizeof(r->reverse_paf[k].length), 1, fp);
r->reverse_paf[k].size = r->reverse_paf[k].length;
r->reverse_paf[k].buffer = NULL;
if(r->reverse_paf[k].length == 0) continue;
r->reverse_paf[k].buffer = (ma_hit_t*)malloc(sizeof(ma_hit_t)*r->reverse_paf[k].length);
fread(r->reverse_paf[k].buffer, sizeof((*(r->reverse_paf[k].buffer))), r->reverse_paf[k].length, fp);
}
}
}
fclose(fp);
@@ -1619,16 +1653,16 @@ void refresh_pt_idx(void **flt_tab, ha_pt_t **ha_idx, All_reads *r, hifiasm_opt_
sprintf(gfa_name, "%s.ad", file_name);
if(is_w) {
write_pt_index(*flt_tab, *ha_idx, NULL, opt, gfa_name);
write_pt_index(*flt_tab, *ha_idx, NULL, opt, gfa_name, 0);
} else {
load_pt_index(flt_tab, ha_idx, NULL, opt, gfa_name);
load_pt_index(flt_tab, ha_idx, NULL, opt, gfa_name, 0);
}
free(gfa_name);
}
uint64_t tmp_pt_pro(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads *r, cc_v* rcc, hifiasm_opt_t *opt, char *file_name, uint64_t rr, uint64_t tot_rr, uint64_t is_load)
uint64_t tmp_pt_pro(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads *r, cc_v* rcc, hifiasm_opt_t *opt, char *file_name, uint64_t rr, uint64_t tot_rr, uint64_t is_load, uint8_t force_rpaf_load)
{
char* gfa_name = (char*)malloc(strlen(file_name)+64);
FILE *fp = NULL; int f_flag = 0; uint64_t rr0 = (uint64_t)-1, tot_rr0 = (uint64_t)-1;
@@ -1649,7 +1683,7 @@ uint64_t tmp_pt_pro(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads *r, cc_v* rc
}
sprintf(gfa_name, "%s.r%lu", file_name, rr);
if(!load_pt_index(r_flt_tab, r_ha_idx, r, opt, gfa_name)) {
if(!load_pt_index(r_flt_tab, r_ha_idx, r, opt, gfa_name, force_rpaf_load)) {
destory_All_reads(r);
ha_pt_destroy(*r_ha_idx); (*r_ha_idx) = NULL;
ha_ft_destroy(*r_flt_tab); (*r_flt_tab) = NULL;
@@ -1673,7 +1707,7 @@ uint64_t tmp_pt_pro(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads *r, cc_v* rc
write_cc_v(rcc, gfa_name);
sprintf(gfa_name, "%s.r%lu", file_name, rr);
write_pt_index(*r_flt_tab, *r_ha_idx, r, opt, gfa_name);
write_pt_index(*r_flt_tab, *r_ha_idx, r, opt, gfa_name, force_rpaf_load);
sprintf(gfa_name, "%s.r%lu.ht.bin", file_name, rr);
fp = fopen(gfa_name, "w");