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fix memory leak of print_utg

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chhylp123
2023-05-12 11:31:34 -04:00
parent 18b649aadb
commit 2c18ec30da
5 changed files with 53 additions and 19 deletions
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22
Assembly.cpp
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@@ -700,6 +700,7 @@ static void worker_ovec_related_reads(void *data, long i, int tid)
if(k < R_INF_FLAG.query_num)
{
R_INF_FLAG.read_id[k] = i;
int fully_cov, abnormal, q_idx = k;
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist,
@@ -766,6 +767,7 @@ static void worker_ovec_related_reads(void *data, long i, int tid)
Get_READ_LENGTH(R_INF, b->olist.list[k].y_id));
}
/**
fprintf(R_INF_FLAG.fp, "***************************unmatched ovlp***************************\n");
for (k = 0; k < b->olist.length; k++)
{
@@ -777,6 +779,7 @@ static void worker_ovec_related_reads(void *data, long i, int tid)
b->olist.list[k].y_pos_strand, b->olist.list[k].strong, b->olist.list[k].without_large_indel,
Get_READ_LENGTH(R_INF, b->olist.list[k].y_id));
}
**/
R_INF.trio_flag[i] = AMBIGU;
@@ -950,6 +953,19 @@ void print_het_cnt_log(uint32_t *het_cnt)
fclose(output_file);
}
void prt_dbg_rs(FILE *fp, Debug_reads* x, uint64_t round)
{
uint64_t k, id; UC_Read g_read; init_UC_Read(&g_read);
for (k = 0; k < R_INF_FLAG.query_num; k++) {
id = x->read_id[k];
if(id == ((uint64_t)-1)) continue;
recover_UC_Read(&g_read, &R_INF, id);
fprintf(fp, ">%.*s_r%lu\n", (int)Get_NAME_LENGTH((R_INF), id), Get_NAME((R_INF), id), round);
fprintf(fp, "%.*s\n", (int)g_read.length, g_read.seq);
}
destory_UC_Read(&g_read);
}
void ha_overlap_and_correct(int round)
{
@@ -999,8 +1015,7 @@ void ha_overlap_and_correct(int round)
ha_ovec_destroy(b[i]);
}
free(b);
if (asm_opt.required_read_name) destory_Debug_reads(&R_INF_FLAG), exit(0); // for debugging only
if (asm_opt.required_read_name) prt_dbg_rs(R_INF_FLAG.fp_r0, &R_INF_FLAG, 0); // for debugging only
// save corrected reads to R_INF
CALLOC(e, asm_opt.thread_num);
@@ -1017,6 +1032,9 @@ void ha_overlap_and_correct(int round)
free(e[i].second_round_read);
}
free(e);
if (asm_opt.required_read_name) prt_dbg_rs(R_INF_FLAG.fp_r1, &R_INF_FLAG, 1); // for debugging only
if (asm_opt.required_read_name) destory_Debug_reads(&R_INF_FLAG), exit(0); // for debugging only
///debug_print_pob_regions();
}