mirror of
https://github.com/chhylp123/hifiasm.git
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89 lines
2.0 KiB
C
89 lines
2.0 KiB
C
#ifndef __KMER__
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#define __KMER__
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#include "Process_Read.h"
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#define ALL (0xffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff)
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#define SAFE_SHIFT(k) k & ((k < 64)?ALL:0)
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static unsigned char seq_nt6_table[256] = {
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
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5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5
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};
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typedef struct
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{
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///最大64-mer
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///x[0]低位
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///x[1]高位
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uint64_t x[2];
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} Hash_code;
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typedef struct
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{
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char* str;
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long long l;
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long long i;
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} HPC_seq;
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inline uint64_t get_HPC_code(HPC_seq* seq)
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{
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if(seq->i < seq ->l)
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{
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char code = seq->str[seq->i];
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for (; seq->i < seq->l; seq->i++)
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{
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if (seq->str[seq->i] != code)
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{
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break;
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}
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}
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return (uint64_t)seq_nt6_table[(uint8_t)code];
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}
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else
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{
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///end
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return 6;
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}
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}
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inline void k_mer_append(Hash_code* code, uint64_t c, int k)
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{
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uint64_t mask = ALL >> (64 -k);
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code->x[0] = ((code->x[0]<<1) | (c&1)) & mask;
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code->x[1] = ((code->x[1]<<1) | (c>>1)) & mask;
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}
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void init_HPC_seq(HPC_seq* seq, char* str, long long l);
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void init_Hash_code(Hash_code* code);
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#endif |