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NOT WORKING!!! removed small_hash_table

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This commit is contained in:
Heng Li
2020-03-24 00:57:00 -04:00
parent 59a9d62df9
commit 398e73022b
3 changed files with 11 additions and 218 deletions
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kmer.h
+7 -26
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@@ -8,38 +8,12 @@
#define SAFE_SHIFT(k) k & ((k < 64)?ALL:0)
/****************************may have bugs********************************/
typedef struct
{
//can represent at most 64-mer
uint64_t x[4];
} Hash_code;
typedef struct {
Hash_code key; ///k-mer itself
uint64_t value; ///offset
} k_v;
typedef struct {
k_v* buffer;
uint32_t size;
uint32_t length;
} small_hash_table;
void init_small_hash_table(small_hash_table* x);
void clear_small_hash_table(small_hash_table* x);
void resize_small_hash_table(small_hash_table* x, uint64_t size);
void destory_small_hash_table(small_hash_table* x);
void add_small_hash_table(small_hash_table* x, k_v* element);
void sort_small_hash_table(small_hash_table* x);
int compare_k_mer(k_v* x, k_v* y);
int query_small_hash_table(small_hash_table* target, k_v* query, long long* l_end, long long* r_end);
typedef struct
{
char* str;
@@ -49,6 +23,13 @@ typedef struct
} HPC_seq;
inline void init_HPC_seq(HPC_seq* seq, char* str, long long l)
{
seq->i = 0;
seq->l = l;
seq->N_occ = 0;
seq->str = str;
}
inline uint64_t get_HPC_code(HPC_seq* seq, uint64_t* end_pos)
{