c_cpp/lib/klib/kbit.h

   1 #ifndef KBIT_H
   2 #define KBIT_H
   3
   4 #include <stdint.h>
   5
   6 static inline uint64_t kbi_popcount64(uint64_t y) // standard popcount; from wikipedia
   7 {
   8         y -= ((y >> 1) & 0x5555555555555555ull);
   9         y = (y & 0x3333333333333333ull) + (y >> 2 & 0x3333333333333333ull);
  10         return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
  11 }
  12
  13 static inline uint64_t kbi_DNAcount64(uint64_t y, int c) // count #A/C/G/T from a 2-bit encoded integer; from BWA
  14 {
  15         // reduce nucleotide counting to bits counting
  16         y = ((c&2)? y : ~y) >> 1 & ((c&1)? y : ~y) & 0x5555555555555555ull;
  17         // count the number of 1s in y
  18         y = (y & 0x3333333333333333ull) + (y >> 2 & 0x3333333333333333ull);
  19         return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
  20 }
  21
  22 #ifndef kroundup32 // round a 32-bit integer to the next closet integer; from "bit twiddling hacks"
  23 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
  24 #endif
  25
  26 #ifndef kbi_swap
  27 #define kbi_swap(a, b) (((a) ^= (b)), ((b) ^= (a)), ((a) ^= (b))) // from "bit twiddling hacks"
  28 #endif
  29
  30 #endif