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fix memory issue

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chhylp123
2024-10-13 18:47:05 -04:00
parent e8b18560a5
commit 49dd83df2a
6 changed files with 235 additions and 33 deletions
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50
htab.cpp
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@@ -1329,7 +1329,7 @@ int load_ct_index(void **i_ct_idx, 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)
{
char* gfa_name = (char*)malloc(strlen(file_name)+25);
char* gfa_name = (char*)malloc(strlen(file_name)+64);
sprintf(gfa_name, "%s.pt_flt", file_name);
FILE* fp = fopen(gfa_name, "w");
if (!fp) {
@@ -1372,15 +1372,29 @@ int write_pt_index(void *flt_tab, ha_pt_t *ha_idx, All_reads* r, hifiasm_opt_t*
write_All_reads(r, gfa_name);
sprintf(gfa_name, "%s.pt_flt.paf.bin", file_name);
fclose(fp); fp = fopen(gfa_name, "w"); uint64_t k;
if (!fp) {
free(gfa_name);
return 0;
}
fwrite(&(r->total_reads), sizeof(r->total_reads), 1, fp);
for (k = 0; k < r->total_reads; k++) {
fwrite(&(r->paf[k].is_fully_corrected), sizeof(r->paf[k].is_fully_corrected), 1, fp);
fwrite(&(r->paf[k].is_abnormal), sizeof(r->paf[k].is_abnormal), 1, fp);
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);
}
fprintf(stderr, "[M::%s] Index has been written.\n", __func__);
free(gfa_name);
fclose(fp);
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)
{
char* gfa_name = (char*)malloc(strlen(file_name)+25);
char* gfa_name = (char*)malloc(strlen(file_name)+64);
sprintf(gfa_name, "%s.pt_flt", file_name);
FILE* fp = fopen(gfa_name, "r");
if (!fp) {
@@ -1460,7 +1474,7 @@ int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads* r, hifiasm_op
f_flag += fread(&opt->max_n_chain, sizeof(opt->max_n_chain), 1, fp);
fclose(fp);
// fclose(fp);
if(!load_All_reads(r, gfa_name))
{
@@ -1468,15 +1482,33 @@ int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads* r, hifiasm_op
return 0;
}
memset(r->trio_flag, AMBIGU, r->total_reads*sizeof(uint8_t));
sprintf(gfa_name, "%s.pt_flt.paf.bin", file_name);
fclose(fp); fp = fopen(gfa_name, "r"); uint64_t k;
if (!fp) {
free(gfa_name);
return 0;
}
f_flag += fread(&(r->total_reads), sizeof(r->total_reads), 1, fp);
r->paf = (ma_hit_t_alloc*)malloc(sizeof(ma_hit_t_alloc)*r->total_reads);
r->reverse_paf = (ma_hit_t_alloc*)malloc(sizeof(ma_hit_t_alloc)*r->total_reads);
for (i = 0; i < (long long)r->total_reads; i++)
{
init_ma_hit_t_alloc(&(r->paf[i]));
init_ma_hit_t_alloc(&(r->reverse_paf[i]));
for (k = 0; k < r->total_reads; k++) {
// init_ma_hit_t_alloc(&(r->paf[k]));
init_ma_hit_t_alloc(&(r->reverse_paf[k]));
f_flag += fread(&(r->paf[k].is_fully_corrected), sizeof(r->paf[k].is_fully_corrected), 1, fp);
f_flag += fread(&(r->paf[k].is_abnormal), sizeof(r->paf[k].is_abnormal), 1, fp);
f_flag += fread(&(r->paf[k].length), sizeof(r->paf[k].length), 1, fp);
r->paf[k].size = r->paf[k].length;
r->paf[k].buffer = NULL;
if(r->paf[k].length == 0) continue;
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);
}
fclose(fp);
fprintf(stderr, "[M::%s] Index has been loaded.\n", __func__);