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backup without bundaries processing

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This commit is contained in:
Haoyu Cheng
2019-12-17 16:58:20 -05:00
parent 90195293f1
commit 06556e4a9b
7 changed files with 2227 additions and 394 deletions
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kmer.h
+17 -1
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@@ -4,8 +4,9 @@
///#define ALL (0xffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff)
#define ALL (0xffffffffffffffff)
/****************************may have bugs********************************/
#define SAFE_SHIFT(k) k & ((k < 64)?ALL:0)
/****************************may have bugs********************************/
@@ -94,6 +95,21 @@ inline void k_mer_append(Hash_code* code, uint64_t c, int k)
code->x[1] = ((code->x[1]<<1) | (c>>1)) & mask;
}
inline void Hashcode_to_string(Hash_code* code, char* str, int k)
{
uint8_t c;
int i;
for (i = 0; i < k; i++)
{
c = (code->x[1] >> (k - i - 1)) & ((uint64_t)1);
c = c << 1;
c = c | ((code->x[0] >> (k - i - 1)) & ((uint64_t)1));
str[i] = s_H[c];
}
}
void init_HPC_seq(HPC_seq* seq, char* str, long long l);
void init_Hash_code(Hash_code* code);