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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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Hash_Table.h
+13 -26
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@@ -80,24 +80,23 @@ typedef struct
typedef struct
{
uint64_t x_id;
uint32_t x_id;
///the begining and end of the whole overlap
uint64_t x_pos_s;
uint64_t x_pos_e;
uint64_t x_pos_strand;
uint32_t x_pos_s;
uint32_t x_pos_e;
uint32_t x_pos_strand;
uint64_t y_id;
uint64_t y_pos_s;
uint64_t y_pos_e;
uint64_t y_pos_strand;
uint32_t y_id;
uint32_t y_pos_s;
uint32_t y_pos_e;
uint32_t y_pos_strand;
uint64_t overlapLen;
uint64_t shared_seed;
uint64_t align_length;
///uint64_t total_errors;
uint32_t overlapLen;
uint32_t shared_seed;
uint32_t align_length;
uint8_t is_match;
uint8_t without_large_indel;
uint64_t non_homopolymer_errors;
uint32_t non_homopolymer_errors;
window_list* w_list;
uint64_t w_list_size;
@@ -163,7 +162,7 @@ void resize_fake_cigar(Fake_Cigar* x, uint64_t size);
int get_fake_gap_pos(Fake_Cigar* x, int index);
int get_fake_gap_shift(Fake_Cigar* x, int index);
inline long long y_start_offset(long long x_start, Fake_Cigar* o)
static inline long long y_start_offset(long long x_start, Fake_Cigar* o)
{
if(x_start == get_fake_gap_pos(o, o->length - 1))
{
@@ -189,18 +188,6 @@ inline long long y_start_offset(long long x_start, Fake_Cigar* o)
return get_fake_gap_shift(o, i - 1);
}
inline void print_fake_gap(Fake_Cigar* o)
{
long long i;
for (i = 0; i < (long long)o->length; i++)
{
fprintf(stderr, "**i: %lld, gap_pos_in_x: %d, gap_shift: %d\n",
i, get_fake_gap_pos(o, i),
get_fake_gap_shift(o, i));
}
}
void resize_Chain_Data(Chain_Data* x, long long size);
void init_window_list_alloc(window_list_alloc* x);
void clear_window_list_alloc(window_list_alloc* x);