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r184: fixed a memory leak in POA

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This commit is contained in:
Heng Li
2020-04-03 14:10:40 -04:00
parent d529dcea3f
commit 6f4d0debe4
2 changed files with 74 additions and 132 deletions
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CommandLines.h
+1 -1
View File
@@ -3,7 +3,7 @@
#include <pthread.h> #include <pthread.h>
#define HA_VERSION "0.3.0-dirty-r183" #define HA_VERSION "0.3.0-dirty-r184"
#define VERBOSE 0 #define VERBOSE 0
#define VERBOSE_GFA 0 #define VERBOSE_GFA 0
POA.cpp
+73 -131
View File
@@ -1,29 +1,27 @@
#include "POA.h"
#include <stdlib.h> #include <stdlib.h>
#include <string.h>
#include "POA.h"
#include "Correct.h" #include "Correct.h"
#include "Process_Read.h" #include "Process_Read.h"
#define INIT_EDGE_SIZE 50 #define INIT_EDGE_SIZE 50
#define INCREASE_EDGE_SIZE 5 #define INCREASE_EDGE_SIZE 5
#define INIT_NODE_SIZE 16000 #define INIT_NODE_SIZE 16000
/********
* Edge *
********/
void init_Edge_alloc(Edge_alloc* list) void init_Edge_alloc(Edge_alloc* list)
{ {
if (list->list == NULL) if (list->list == NULL) {
{ list->size = INIT_EDGE_SIZE;
list->size = INIT_EDGE_SIZE; list->length = 0;
list->length = 0; list->delete_length = 0;
list->delete_length = 0; list->list = (Edge*)malloc(sizeof(Edge)*list->size);
list->list = (Edge*)malloc(sizeof(Edge)*list->size); } else {
} list->length = 0;
else list->delete_length = 0;
{ }
list->length = 0;
list->delete_length = 0;
}
} }
void clear_Edge_alloc(Edge_alloc* list) void clear_Edge_alloc(Edge_alloc* list)
@@ -34,28 +32,29 @@ void clear_Edge_alloc(Edge_alloc* list)
void destory_Edge_alloc(Edge_alloc* list) void destory_Edge_alloc(Edge_alloc* list)
{ {
free(list->list); if (list && list->list)
free(list->list);
} }
void append_Edge_alloc(Edge_alloc* list, uint64_t in_node, uint64_t out_node, uint64_t weight, uint64_t length) void append_Edge_alloc(Edge_alloc* list, uint64_t in_node, uint64_t out_node, uint64_t weight, uint64_t length)
{ {
if (list->length + 1 > list->size) if (list->length + 1 > list->size) {
{ uint64_t old_size = list->size;
list->size = list->size + INCREASE_EDGE_SIZE; list->size = list->size + INCREASE_EDGE_SIZE;
list->list = (Edge*)realloc(list->list, sizeof(Edge)*list->size); list->list = (Edge*)realloc(list->list, sizeof(Edge)*list->size);
} memset(&list->list[old_size], 0, (list->size - old_size) * sizeof(Edge));
}
list->list[list->length].in_node = in_node; list->list[list->length].in_node = in_node;
list->list[list->length].out_node = out_node; list->list[list->length].out_node = out_node;
list->list[list->length].weight = weight; list->list[list->length].weight = weight;
list->list[list->length].length = length; list->list[list->length].length = length;
list->list[list->length].num_insertions = 0; list->list[list->length].num_insertions = 0;
list->list[list->length].self_edge_ID = list->length; list->list[list->length].self_edge_ID = list->length;
list->length++; list->length++;
} }
int add_and_check_bi_direction_edge(Graph* graph, Node* in_node, Node* out_node, uint64_t weight, uint64_t flag) int add_and_check_bi_direction_edge(Graph* graph, Node* in_node, Node* out_node, uint64_t weight, uint64_t flag)
{ {
Edge* e_forward; Edge* e_forward;
@@ -81,7 +80,6 @@ int add_and_check_bi_direction_edge(Graph* graph, Node* in_node, Node* out_node,
} }
} }
void add_bi_direction_edge(Graph* graph, Node* in_node, Node* out_node, uint64_t weight, uint64_t flag) void add_bi_direction_edge(Graph* graph, Node* in_node, Node* out_node, uint64_t weight, uint64_t flag)
{ {
@@ -95,8 +93,6 @@ void add_bi_direction_edge(Graph* graph, Node* in_node, Node* out_node, uint64_t
= Output_Edges((*in_node)).length - 1; = Output_Edges((*in_node)).length - 1;
} }
int remove_and_check_bi_direction_edge_from_nodes(Graph* graph, Node* in_node, Node* out_node) int remove_and_check_bi_direction_edge_from_nodes(Graph* graph, Node* in_node, Node* out_node)
{ {
Edge* e_forward; Edge* e_forward;
@@ -135,8 +131,6 @@ int remove_and_check_bi_direction_edge_from_nodes(Graph* graph, Node* in_node, N
} }
} }
int remove_and_check_bi_direction_edge_from_edge(Graph* graph, Edge* e) int remove_and_check_bi_direction_edge_from_edge(Graph* graph, Edge* e)
{ {
Edge* e_forward; Edge* e_forward;
@@ -171,109 +165,71 @@ int remove_and_check_bi_direction_edge_from_edge(Graph* graph, Edge* e)
{ {
return 0; return 0;
} }
} }
/********
* Node *
********/
void init_Node_alloc(Node_alloc* list) void init_Node_alloc(Node_alloc* list)
{ {
list->size = INIT_NODE_SIZE; memset(list, 0, sizeof(Node_alloc));
list->length = 0; list->size = INIT_NODE_SIZE;
list->delete_length = 0; list->list = (Node*)calloc(list->size, sizeof(Node));
list->list = (Node*)malloc(sizeof(Node)*list->size);
list->sort.size = 0;
list->sort.list = NULL;
list->sort.visit = NULL;
list->sort.iterative_buffer = NULL;
list->sort.iterative_buffer_visit = NULL;
uint64_t i;
for (i = 0; i < list->size; i++)
{
list->list[i].insertion_edges.list=NULL;
list->list[i].mismatch_edges.list=NULL;
list->list[i].deletion_edges.list=NULL;
}
} }
void destory_Node_alloc(Node_alloc* list) void destory_Node_alloc(Node_alloc* list)
{ {
uint64_t i =0; uint64_t i;
for (i = 0; i < list->length; i++) for (i = 0; i < list->size; i++) {
{ destory_Edge_alloc(&list->list[i].deletion_edges);
destory_Edge_alloc(&list->list[i].deletion_edges); destory_Edge_alloc(&list->list[i].insertion_edges);
destory_Edge_alloc(&list->list[i].insertion_edges); destory_Edge_alloc(&list->list[i].mismatch_edges);
destory_Edge_alloc(&list->list[i].mismatch_edges); }
} free(list->list);
free(list->sort.list);
free(list->list); free(list->sort.visit);
free(list->sort.list); free(list->sort.iterative_buffer);
free(list->sort.visit); free(list->sort.iterative_buffer_visit);
free(list->sort.iterative_buffer);
free(list->sort.iterative_buffer_visit);
///free(list->topo_order);
} }
void clear_Node_alloc(Node_alloc* list) void clear_Node_alloc(Node_alloc* list)
{ {
uint64_t i =0; uint64_t i =0;
for (i = 0; i < list->length; i++) for (i = 0; i < list->length; i++) { // TODO: is this list->size or list->length? The original version is list->length.
{ clear_Edge_alloc(&list->list[i].insertion_edges);
clear_Edge_alloc(&list->list[i].insertion_edges); clear_Edge_alloc(&list->list[i].mismatch_edges);
clear_Edge_alloc(&list->list[i].mismatch_edges); clear_Edge_alloc(&list->list[i].deletion_edges);
clear_Edge_alloc(&list->list[i].deletion_edges); }
} list->length = 0;
list->delete_length = 0;
list->length = 0;
list->delete_length = 0;
} }
uint64_t append_Node_alloc(Node_alloc* list, char base) uint64_t append_Node_alloc(Node_alloc* list, char base)
{ {
if (list->length + 1 > list->size) {
if (list->length + 1 > list->size) uint64_t old_size = list->size;
{ list->size = list->size * 2;
uint64_t i = list->size; list->list = (Node*)realloc(list->list, sizeof(Node) * list->size);
memset(&list->list[old_size], 0, (list->size - old_size) * sizeof(Node));
}
list->size = list->size * 2; list->list[list->length].ID = list->length;
list->list = (Node*)realloc(list->list, sizeof(Node)*list->size); list->list[list->length].base = base;
///list->topo_order = (uint64_t*)realloc(list->topo_order, sizeof(uint64_t)*list->size); list->list[list->length].weight = 1;
list->list[list->length].num_insertions = 0;
for (; i < list->size; i++) init_Edge_alloc(&list->list[list->length].deletion_edges);
{ init_Edge_alloc(&list->list[list->length].insertion_edges);
list->list[i].deletion_edges.list=NULL; init_Edge_alloc(&list->list[list->length].mismatch_edges);
list->list[i].insertion_edges.list=NULL;
list->list[i].mismatch_edges.list=NULL;
}
}
list->list[list->length].ID = list->length;
list->list[list->length].base = base;
list->list[list->length].weight = 1;
list->list[list->length].num_insertions = 0;
init_Edge_alloc(&list->list[list->length].deletion_edges);
init_Edge_alloc(&list->list[list->length].insertion_edges);
init_Edge_alloc(&list->list[list->length].mismatch_edges);
list->length++;
return list->length - 1; list->length++;
return list->length - 1;
} }
/*********
* Graph *
*********/
void init_Graph(Graph* g) void init_Graph(Graph* g)
{ {
@@ -310,12 +266,6 @@ void clear_Graph(Graph* g)
clear_Queue(&(g->node_q)); clear_Queue(&(g->node_q));
} }
void addUnmatchedSeqToGraph(Graph* g, char* g_read_seq, long long g_read_length, long long* startID, long long* endID) void addUnmatchedSeqToGraph(Graph* g, char* g_read_seq, long long g_read_length, long long* startID, long long* endID)
{ {
long long firstID, lastID, nodeID, i; long long firstID, lastID, nodeID, i;
@@ -356,8 +306,6 @@ void addUnmatchedSeqToGraph(Graph* g, char* g_read_seq, long long g_read_length,
} }
void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_string, long long x_length, void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_string, long long x_length,
char* y_string, long long y_length, CIGAR* cigar, long long backbone_start, long long backbone_end) char* y_string, long long y_length, CIGAR* cigar, long long backbone_start, long long backbone_end)
{ {
@@ -422,9 +370,3 @@ void addmatchedSeqToGraph(Graph* backbone, long long currentNodeID, char* x_stri
cigar_i++; cigar_i++;
} }
} }