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r186: fixed memory leaks when loading from disk

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This commit is contained in:
Heng Li
2020-04-03 20:35:47 -04:00
parent 992322f8e3
commit 76de054331
6 changed files with 24 additions and 52 deletions
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Assembly.cpp
-1
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@@ -1299,7 +1299,6 @@ void ha_overlap_final(void)
ha_idx = 0;
///rescue_edges(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads, 4, 0.985);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> final overlap\n", __func__, yak_realtime(), yak_cputime() / yak_realtime());
}
int ha_assemble(void)
CommandLines.h
+1 -1
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@@ -3,7 +3,7 @@
#include <pthread.h>
#define HA_VERSION "0.3.0-dirty-r185"
#define HA_VERSION "0.3.0-dirty-r186"
#define VERBOSE 0
#define VERBOSE_GFA 0
Overlaps.cpp
+15 -24
View File
@@ -13398,8 +13398,6 @@ 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);
@@ -13466,35 +13464,28 @@ 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))
{
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))
{
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))
{
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;
}
return 0;
}
free(gfa_name);
return 1;
return 1;
}
// count the number of outgoing arcs, excluding reduced arcs
static inline int count_out(const asg_t *g, uint32_t v)
{
Overlaps.h
+1 -4
View File
@@ -47,9 +47,6 @@
#define CUT_DIF_HAP 12
///query is the read itself
typedef struct {
uint64_t qns;
@@ -1033,4 +1030,4 @@ uint32_t is_bubble_check, uint32_t is_primary_check);
uint32_t get_edge_from_source(ma_hit_t_alloc* sources, ma_sub_t *coverage_cut,
R_to_U* ruIndex, int max_hang, int min_ovlp, uint32_t query, uint32_t target, asg_arc_t* t);
#endif
#endif
Process_Read.cpp
+7 -21
View File
@@ -1,9 +1,8 @@
#include "Process_Read.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <fcntl.h>
#include <pthread.h>
#include "Process_Read.h"
uint8_t seq_nt6_table[256] = {
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
@@ -29,34 +28,28 @@ char bit_t_seq_table_rc[256][4] = {{0}};
char s_H[5] = {'A', 'C', 'G', 'T', 'N'};
char rc_Table[5] = {'T', 'G', 'C', 'A', 'N'};
void init_All_reads(All_reads* r)
{
memset(r, 0, sizeof(All_reads));
r->index_size = READ_INIT_NUMBER;
r->read_length = (uint64_t*)malloc(sizeof(uint64_t)*r->index_size);
r->read_sperate = NULL;
r->N_site = NULL;
r->total_reads_bases = 0;
r->name_index_size = READ_INIT_NUMBER;
r->name_index = (uint64_t*)malloc(sizeof(uint64_t)*r->name_index_size);
r->name_index[0] = 0;
r->name = NULL;
r->total_name_length = 0;
r->total_reads = 0;
r->trio_flag = NULL;
}
void destory_All_reads(All_reads* r)
{
uint64_t i = 0;
for (i = 0; i < r->total_reads; i++)
{
for (i = 0; i < r->total_reads; i++) {
if (r->N_site[i] != NULL)
{
free(r->N_site[i]);
}
free(r->read_sperate[i]);
if (r->paf) free(r->paf[i].buffer);
if (r->reverse_paf) free(r->reverse_paf[i].buffer);
}
free(r->paf);
free(r->reverse_paf);
free(r->N_site);
free(r->read_sperate);
free(r->name);
@@ -114,7 +107,6 @@ void write_All_reads(All_reads* r, char* read_file_name)
int load_All_reads(All_reads* r, char* read_file_name)
{
//fprintf(stderr, "Loading reads from disk... \n");
char* index_name = (char*)malloc(strlen(read_file_name)+15);
sprintf(index_name, "%s.bin", read_file_name);
FILE* fp = fopen(index_name, "r");
@@ -146,7 +138,6 @@ int load_All_reads(All_reads* r, char* read_file_name)
if (zero)
{
r->N_site[i] = (uint64_t*)malloc(sizeof(uint64_t)*(zero + 1));
r->N_site[i][0] = zero;
if (r->N_site[i][0])
@@ -158,7 +149,6 @@ int load_All_reads(All_reads* r, char* read_file_name)
{
r->N_site[i] = NULL;
}
}
r->read_length = (uint64_t*)malloc(sizeof(uint64_t)*r->total_reads);
@@ -188,8 +178,6 @@ int load_All_reads(All_reads* r, char* read_file_name)
r->cigars = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
r->second_round_cigar = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
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 < r->total_reads; i++)
{
r->second_round_cigar[i].size = r->cigars[i].size = 0;
@@ -199,8 +187,6 @@ int load_All_reads(All_reads* r, char* read_file_name)
r->second_round_cigar[i].lost_base_size = r->cigars[i].lost_base_size = 0;
r->second_round_cigar[i].lost_base_length = r->cigars[i].lost_base_length = 0;
r->second_round_cigar[i].lost_base = r->cigars[i].lost_base = NULL;
init_ma_hit_t_alloc(&(r->paf[i]));
init_ma_hit_t_alloc(&(r->reverse_paf[i]));
}
free(index_name);
Process_Read.h
-1
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@@ -128,7 +128,6 @@ typedef struct
ma_hit_t_alloc* paf;
ma_hit_t_alloc* reverse_paf;
ma_sub_t* coverage_cut;
} All_reads;
extern All_reads R_INF;