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r179: replace one qsort() with ks_introsort()

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This commit is contained in:
Heng Li
2020-04-02 10:34:43 -04:00
parent 7776dee103
commit 483ceb852c
5 changed files with 20 additions and 91 deletions
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65
Hash_Table.cpp
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@@ -12,6 +12,9 @@ pthread_mutex_t output_mutex;
#define overlap_region_key(a) ((a).y_id)
KRADIX_SORT_INIT(overlap_region_sort, overlap_region, overlap_region_key, member_size(overlap_region, y_id))
#define oreg_xs_lt(a, b) (((uint64_t)(a).x_pos_s<<32|(a).x_pos_e) < ((uint64_t)(b).x_pos_s<<32|(b).x_pos_e))
KSORT_INIT(or_xs, overlap_region, oreg_xs_lt)
void overlap_region_sort_y_id(overlap_region *a, long long n)
{
radix_sort_overlap_region_sort(a, a + n);
@@ -30,6 +33,7 @@ void init_overlap_region_alloc(overlap_region_alloc* list)
init_window_list_alloc(&(list->list[i].boundary_cigars));
}
}
void clear_overlap_region_alloc(overlap_region_alloc* list)
{
list->length = 0;
@@ -58,7 +62,6 @@ void destory_overlap_region_alloc(overlap_region_alloc* list)
free(list->list);
}
int get_fake_gap_pos(Fake_Cigar* x, int index)
{
return (x->buffer[index]>>32);
@@ -269,64 +272,6 @@ void append_overlap_region_alloc_debug(overlap_region_alloc* list, overlap_regio
list->length++;
}
int cmp_by_x_pos_s(const void * a, const void * b)
{
if ((*(overlap_region*)a).x_pos_s > (*(overlap_region*)b).x_pos_s)
{
return 1;
}
else if ((*(overlap_region*)a).x_pos_s < (*(overlap_region*)b).x_pos_s)
{
return -1;
}
else
{
if ((*(overlap_region*)a).x_pos_e > (*(overlap_region*)b).x_pos_e)
{
return 1;
}
else if ((*(overlap_region*)a).x_pos_e < (*(overlap_region*)b).x_pos_e)
{
return -1;
}
else
{
return 0;
}
}
}
int cmp_by_x_pos_e(const void * a, const void * b)
{
if ((*(overlap_region*)a).x_pos_e > (*(overlap_region*)b).x_pos_e)
{
return 1;
}
else if ((*(overlap_region*)a).x_pos_e < (*(overlap_region*)b).x_pos_e)
{
return -1;
}
else
{
if ((*(overlap_region*)a).x_pos_s > (*(overlap_region*)b).x_pos_s)
{
return 1;
}
else if ((*(overlap_region*)a).x_pos_s < (*(overlap_region*)b).x_pos_s)
{
return -1;
}
else
{
return 0;
}
}
}
void debug_chain(k_mer_hit* a, long long a_n, Chain_Data* dp)
{
long long i, j, current_j;
@@ -709,7 +654,7 @@ void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_r
destory_fake_cigar(&(tmp_region.f_cigar));
qsort(overlap_list->list, overlap_list->length, sizeof(overlap_region), cmp_by_x_pos_s);
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}
void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,