mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-27 08:58:11 +08:00
82 lines
1.8 KiB
C
82 lines
1.8 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 ALL (0xffffffffffffffff)
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/****************************may have bugs********************************/
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#define SAFE_SHIFT(k) k & ((k < 64)?ALL:0)
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/****************************may have bugs********************************/
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typedef struct
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{
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//can represent at most 64-mer
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uint64_t x[4];
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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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long long N_occ;
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} HPC_seq;
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inline void init_HPC_seq(HPC_seq* seq, char* str, long long l)
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{
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seq->i = 0;
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seq->l = l;
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seq->N_occ = 0;
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seq->str = str;
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}
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inline uint64_t get_HPC_code(HPC_seq* seq, uint64_t* end_pos)
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{
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if(seq->i < seq ->l)
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{
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uint8_t code = seq_nt6_table[(uint8_t)seq->str[seq->i]];
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(*end_pos) = seq->i;
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for (; seq->i < seq->l; seq->i++)
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{
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///number of Ns
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if (seq_nt6_table[(uint8_t)seq->str[seq->i]] >= 4)
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{
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seq->N_occ++;
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}
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if (seq_nt6_table[(uint8_t)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)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 init_Hash_code(Hash_code* code)
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{
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code->x[0] = code->x[1] = code->x[2] = code->x[3] = 0;
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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), shift = k - 1;
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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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code->x[2] = code->x[2] >> 1 | (uint64_t)(1 - (c&1)) << shift;
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code->x[3] = code->x[3] >> 1 | (uint64_t)(1 - (c>>1)) << shift;
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}
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#endif
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