/usr/include/kmer/mers.h is in libmeryl-dev 0~20150903+r2013-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 | #ifndef BIO_MERS_H
#define BIO_MERS_H
inline
uint64
reverseComplementMer(uint32 ms, uint64 fmer) {
// The interested reader shall consult bri-bits.h
// Reverse the mer
//
uint64 rmer = fmer;
rmer = ((rmer >> 2) & 0x3333333333333333llu) | ((rmer << 2) & 0xccccccccccccccccllu);
rmer = ((rmer >> 4) & 0x0f0f0f0f0f0f0f0fllu) | ((rmer << 4) & 0xf0f0f0f0f0f0f0f0llu);
rmer = ((rmer >> 8) & 0x00ff00ff00ff00ffllu) | ((rmer << 8) & 0xff00ff00ff00ff00llu);
rmer = ((rmer >> 16) & 0x0000ffff0000ffffllu) | ((rmer << 16) & 0xffff0000ffff0000llu);
rmer = ((rmer >> 32) & 0x00000000ffffffffllu) | ((rmer << 32) & 0xffffffff00000000llu);
// Complement the bases
//
rmer ^= 0xffffffffffffffffllu;
// Shift and mask out the bases not in the mer
//
rmer >>= 64 - ms * 2;
rmer &= uint64MASK(ms * 2);
return(rmer);
}
// Used for in seagen/encodedQuery.C (diagnostics) and
// libbio/kmerhuge.H (in its merToString method).
inline
char *
uint64ToMerString(uint32 ms, uint64 mer, char *str) {
for (uint32 i=0; i<ms; i++)
str[ms-i-1] = bitsToLetter[(mer >> (2*i)) & 0x03];
str[ms] = 0;
return(str);
}
#if 0
#error this is not used anywhere
inline
uint64
stringToMer(uint32 ms, char *str) {
uint64 mer = 0L;
for (uint32 i=0; i<ms; i++) {
mer <<= 2;
mer |= compressSymbol[str[i]];
}
return(mer);
}
#endif
#endif // BIO_MERS_H
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