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kmer.h
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#ifndef PLS_CHAIN_KMER_H
#define PLS_CHAIN_KMER_H
#include "khash.h"
// A 065 01000001
// C 067 01000011
// G 071 01000111
// T 084 01010100
khint64_t lookup_table[256] = {
0b10101010, 0b11101010, 0b00101010, 0b01101010, 0b10111010, 0b11111010, 0b00111010, 0b01111010,
0b10001010, 0b11001010, 0b00001010, 0b01001010, 0b10011010, 0b11011010, 0b00011010, 0b01011010,
0b10101110, 0b11101110, 0b00101110, 0b01101110, 0b10111110, 0b11111110, 0b00111110, 0b01111110,
0b10001110, 0b11001110, 0b00001110, 0b01001110, 0b10011110, 0b11011110, 0b00011110, 0b01011110,
0b10100010, 0b11100010, 0b00100010, 0b01100010, 0b10110010, 0b11110010, 0b00110010, 0b01110010,
0b10000010, 0b11000010, 0b00000010, 0b01000010, 0b10010010, 0b11010010, 0b00010010, 0b01010010,
0b10100110, 0b11100110, 0b00100110, 0b01100110, 0b10110110, 0b11110110, 0b00110110, 0b01110110,
0b10000110, 0b11000110, 0b00000110, 0b01000110, 0b10010110, 0b11010110, 0b00010110, 0b01010110,
0b10101011, 0b11101011, 0b00101011, 0b01101011, 0b10111011, 0b11111011, 0b00111011, 0b01111011,
0b10001011, 0b11001011, 0b00001011, 0b01001011, 0b10011011, 0b11011011, 0b00011011, 0b01011011,
0b10101111, 0b11101111, 0b00101111, 0b01101111, 0b10111111, 0b11111111, 0b00111111, 0b01111111,
0b10001111, 0b11001111, 0b00001111, 0b01001111, 0b10011111, 0b11011111, 0b00011111, 0b01011111,
0b10100011, 0b11100011, 0b00100011, 0b01100011, 0b10110011, 0b11110011, 0b00110011, 0b01110011,
0b10000011, 0b11000011, 0b00000011, 0b01000011, 0b10010011, 0b11010011, 0b00010011, 0b01010011,
0b10100111, 0b11100111, 0b00100111, 0b01100111, 0b10110111, 0b11110111, 0b00110111, 0b01110111,
0b10000111, 0b11000111, 0b00000111, 0b01000111, 0b10010111, 0b11010111, 0b00010111, 0b01010111,
0b10101000, 0b11101000, 0b00101000, 0b01101000, 0b10111000, 0b11111000, 0b00111000, 0b01111000,
0b10001000, 0b11001000, 0b00001000, 0b01001000, 0b10011000, 0b11011000, 0b00011000, 0b01011000,
0b10101100, 0b11101100, 0b00101100, 0b01101100, 0b10111100, 0b11111100, 0b00111100, 0b01111100,
0b10001100, 0b11001100, 0b00001100, 0b01001100, 0b10011100, 0b11011100, 0b00011100, 0b01011100,
0b10100000, 0b11100000, 0b00100000, 0b01100000, 0b10110000, 0b11110000, 0b00110000, 0b01110000,
0b10000000, 0b11000000, 0b00000000, 0b01000000, 0b10010000, 0b11010000, 0b00010000, 0b01010000,
0b10100100, 0b11100100, 0b00100100, 0b01100100, 0b10110100, 0b11110100, 0b00110100, 0b01110100,
0b10000100, 0b11000100, 0b00000100, 0b01000100, 0b10010100, 0b11010100, 0b00010100, 0b01010100,
0b10101001, 0b11101001, 0b00101001, 0b01101001, 0b10111001, 0b11111001, 0b00111001, 0b01111001,
0b10001001, 0b11001001, 0b00001001, 0b01001001, 0b10011001, 0b11011001, 0b00011001, 0b01011001,
0b10101101, 0b11101101, 0b00101101, 0b01101101, 0b10111101, 0b11111101, 0b00111101, 0b01111101,
0b10001101, 0b11001101, 0b00001101, 0b01001101, 0b10011101, 0b11011101, 0b00011101, 0b01011101,
0b10100001, 0b11100001, 0b00100001, 0b01100001, 0b10110001, 0b11110001, 0b00110001, 0b01110001,
0b10000001, 0b11000001, 0b00000001, 0b01000001, 0b10010001, 0b11010001, 0b00010001, 0b01010001,
0b10100101, 0b11100101, 0b00100101, 0b01100101, 0b10110101, 0b11110101, 0b00110101, 0b01110101,
0b10000101, 0b11000101, 0b00000101, 0b01000101, 0b10010101, 0b11010101, 0b00010101, 0b01010101};
khint64_t revComp(khint64_t x, khint64_t mask, size_t k)
{
khint64_t res;
res = lookup_table[x & 0xFF] << 56 |
lookup_table[(x >> 8) & 0xFF] << 48 |
lookup_table[(x >> 16) & 0xFF] << 40 |
lookup_table[(x >> 24) & 0xFF] << 32 |
lookup_table[(x >> 32) & 0xFF] << 24 |
lookup_table[(x >> 40) & 0xFF] << 16 |
lookup_table[(x >> 48) & 0xFF] << 8 |
lookup_table[(x >> 56) & 0xFF];
res = (res >> (64 - 2*k)) & mask;
return res;
}
void my_itoa(khint64_t key, char * buffer){
for (int i = 0; i < 64; i ++){
if ((key & 0b1) == 0b1){
buffer[63-i] = '1';
} else {
buffer[63-i] = '0';
}
key = (key >> 1);
}
buffer[64] = '\0';
}
#endif