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#ifndef UTILITY_FUNCTIONS_HPP
#define UTILITY_FUNCTIONS_HPP
#include <limits>
#include "SalmonUtils.hpp"
// from http://stackoverflow.com/questions/17719674/c11-fast-constexpr-integer-powers
constexpr int64_t constExprPow(int64_t base, unsigned int exp, int64_t result = 1) {
return exp < 1 ? result : constExprPow(base*base, exp/2, (exp % 2) ? result*base : result);
}
inline std::string kmerForIndex(uint32_t idx, uint32_t K) {
std::string kmer(K, 'X');
// The number of bits we need to shift the
// current mask to the left.
uint32_t pos{0};
for (int32_t i = K - 1; i >= 0; --i) {
uint8_t c = (idx >> pos) & 0x3;
switch (c) {
case 0:
kmer[i] = 'A';
break;
case 1:
kmer[i] = 'C';
break;
case 2:
kmer[i] = 'G';
break;
case 3:
kmer[i] = 'T';
break;
default:
break;
}
pos += 2;
}
return kmer;
}
inline uint32_t nextKmerIndex(uint32_t idx, char n, uint32_t K,
salmon::utils::Direction dir) {
using salmon::utils::Direction;
if(dir == Direction::REVERSE or dir == Direction::REVERSE_COMPLEMENT) {
// drop the leftmost character, and replace it with the complement of the
// new one.
idx = idx >> 2;
switch(n) {
case 'A':
case 'a':
// n='T';
// complement is 'T';
idx = idx | (3 << 2*(K-1));
break;
case 'C':
case 'c':
// n='G';
// complement is 'G';
idx = idx | (2 << 2*(K-1));
break;
case 'g':
case 'G':
// n='C';
// complement is 'C';
idx = idx | (1 << 2*(K-1));
break;
case 'T':
case 't':
case 'U':
case 'u':
// n='A';
// complement is 'A';
break;
}
return idx;
} else {
// drop the rightmost character and replace it with the new one.
idx = idx << 2;
switch(n) {
case 'A':
case 'a': break;
case 'C':
case 'c': idx = idx + 1;
break;
case 'G':
case 'g': idx = idx + 2;
break;
case 'T':
case 't':
case 'U':
case 'u':
idx = idx + 3;
break;
}
// Clear the top 32 - 2*K bits.
uint32_t clearShift = (32 - 2*K);
return idx & (0xFFFFFFFF >> clearShift);
}
}
inline uint32_t indexForKmer(const char* s,
uint32_t K,
salmon::utils::Direction dir) {
using salmon::utils::Direction;
// The index we'll return
uint32_t idx{0};
// The number of bits we need to shift the
// current mask to the left.
if(dir == Direction::FORWARD) {
for (int32_t i = 0; i < K; ++i) {
switch (s[i]) {
case 'A':
case 'a':
break;
case 'C':
case 'c':
idx += 1;
break;
case 'G':
case 'g':
idx += 2;
break;
case 'T':
case 't':
case 'U':
case 'u':
idx += 3;
break;
default:
return std::numeric_limits<uint32_t>::max();
}
if (i < K - 1) {idx = idx << 2;}
}
} else {
for(int32_t i=K-1 ; i>=0 ; i--) {
switch(s[i]) {
case 'T':
case 't':
case 'u':
case 'U': break;
case 'C':
case 'c': idx += 2;
break;
case 'G':
case 'g': idx += 1;
break;
case 'A':
case 'a': idx += 3;
break;
default:
return std::numeric_limits<uint32_t>::max();
}
if (i > 0) {idx = idx << 2;}
}
}
return idx;
}
#endif //UTILITY_FUNCTIONS_HPP
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