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smaller memory requirement

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chhylp123
2022-05-12 16:15:58 -04:00
parent dd8888aa90
commit a2198891e7
8 changed files with 1345 additions and 2581 deletions
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Hash_Table.cpp
+25 -66
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@@ -24,9 +24,9 @@ void init_overlap_region_alloc(overlap_region_alloc* list)
///list->list = (overlap_region*)malloc(sizeof(overlap_region)*list->size);
list->list = (overlap_region*)calloc(list->size, sizeof(overlap_region));
uint64_t i;
for (i = 0; i < list->size; i++)
{
for (i = 0; i < list->size; i++) {
init_fake_cigar(&(list->list[i].f_cigar));
init_window_list_alloc(&(list->list[i].w_list));
init_window_list_alloc(&(list->list[i].boundary_cigars));
}
}
@@ -36,10 +36,9 @@ void clear_overlap_region_alloc(overlap_region_alloc* list)
list->length = 0;
list->mapped_overlaps_length = 0;
uint64_t i = 0;
for (i = 0; i < list->size; i++)
{
list->list[i].w_list_length = 0;
for (i = 0; i < list->size; i++) {
clear_fake_cigar(&(list->list[i].f_cigar));
clear_window_list_alloc(&(list->list[i].w_list));
clear_window_list_alloc(&(list->list[i].boundary_cigars));
}
}
@@ -47,30 +46,14 @@ void clear_overlap_region_alloc(overlap_region_alloc* list)
void destory_overlap_region_alloc(overlap_region_alloc* list)
{
uint64_t i = 0;
for (i = 0; i < list->size; i++)
{
if (list->list[i].w_list_size != 0)
{
free(list->list[i].w_list);
}
for (i = 0; i < list->size; i++) {
destory_fake_cigar(&(list->list[i].f_cigar));
destory_window_list_alloc(&(list->list[i].w_list));
destory_window_list_alloc(&(list->list[i].boundary_cigars));
}
free(list->list);
}
void destory_overlap_region_alloc_buf(void *km, overlap_region_alloc* list, int is_z)
{
uint64_t i = 0;
for (i = 0; i < list->size; i++) {
if(list->list[i].w_list_size>0) kfree(km, list->list[i].w_list);
if(list->list[i].f_cigar.size>0) kfree(km, list->list[i].f_cigar.buffer);
if(list->list[i].boundary_cigars.size>0) kfree(km, list->list[i].boundary_cigars.buffer);
}
kfree(km, list->list);
if(is_z) memset(list, 0, sizeof(*list));
}
int get_fake_gap_pos(Fake_Cigar* x, int index)
{
return (x->buffer[index]>>32);
@@ -910,32 +893,18 @@ void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_r
void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
int extra_begin, int extra_end, int error_threshold, int blockLen, void *km)
{
long long length = region->x_pos_e - region->x_pos_s + 1;
///the length of window may large or small than WINDOW
/****************************may have bugs********************************/
uint64_t num_windows = length / blockLen + 4;
/****************************may have bugs********************************/
window_list *p = NULL;
kv_pushp(window_list, region->w_list, &p);
///w_list_length has alredy set to be 0 at clear_overlap_region_alloc
if (num_windows > region->w_list_size)
{
region->w_list_size = num_windows;
if(!km) REALLOC(region->w_list, region->w_list_size);
else KREALLOC(km, region->w_list, region->w_list_size);
}
region->w_list[region->w_list_length].x_start = x_start;
region->w_list[region->w_list_length].x_end = x_end;
region->w_list[region->w_list_length].y_start = y_start;
region->w_list[region->w_list_length].y_end = y_end;
region->w_list[region->w_list_length].error = error;
region->w_list[region->w_list_length].cigar.length = -1;
region->w_list[region->w_list_length].extra_begin = extra_begin;
region->w_list[region->w_list_length].extra_end = extra_end;
region->w_list[region->w_list_length].error_threshold = error_threshold;
region->w_list_length++;
p->x_start = x_start;
p->x_end = x_end;
p->y_start = y_start;
p->y_end = y_end;
p->error = error;
p->extra_begin = extra_begin;
p->extra_end = extra_end;
p->error_threshold = error_threshold;
p->cidx = p->clen = 0;
}
void test_single_list(Candidates_list* candidates, k_mer_pos* n_list, uint64_t n_lengh, uint64_t end_pos, uint64_t strand)
@@ -1118,33 +1087,23 @@ void resize_fake_cigar(Fake_Cigar* x, uint64_t size, void *km)
void init_window_list_alloc(window_list_alloc* x)
{
x->buffer = NULL;
x->length = 0;
x->size = 0;
memset(x, 0, sizeof((*x)));
}
void clear_window_list_alloc(window_list_alloc* x)
{
x->length = 0;
x->n = x->c.n = 0;
}
void destory_window_list_alloc(window_list_alloc* x)
{
if(x->size != 0)
{
free((x->buffer));
}
free(x->a); free(x->c.a);
}
void resize_window_list_alloc(window_list_alloc* x, long long size, void *km)
void resize_window_list_alloc(window_list_alloc* x, uint64_t size)
{
if(size > x->size){
x->size = size;
if(!km) REALLOC(x->buffer, x->size);
else KREALLOC(km, x->buffer, x->size);
}
long long i;
for (i = 0; i < x->size; i++) x->buffer[i].error = -1;
x->length = 0;
kv_resize(window_list, *x, size); x->n = x->c.n = 0;
uint64_t k;
for (k = 0; k < x->m; k++) x->a[k].error = -1;
x->c.n = 0;
}