c++ - Is there a generalization of std::bitset for two-bit values? -

c++ - Is there a generalization of std::bitset for two-bit values? -

suppose genome scientist trying store extremely long strings of characters, each of represents 2 bits of info (i.e. each element either g, a, t, or c). because strings incredibly long, need able store string of length n in exactly 2n bits (or rather, n/4 bytes).

with motivation in mind, looking generalization of std::bitset (or boost::dynamic_bitset<>) works on two-bit values instead of single-bit values. want store n such two-bit values, each of can 0, 1, 2, or 3. need info packed closely possible in memory, vector<char> not work (as wastes factor of 4 of memory).

what best way accomplish goal? 1 alternative wrap existing bitset templates customized operator[], iterators, etc., i'd prefer utilize existing library if @ possible.

you have 2 choices.

given:

enum class nucleobase { a, c, g, t };

you have 2 choices. can:

use single std::bitset , play indexing use std::bitset in combination container

for first, can define couple of functions target right number of bits per set/get:

template<std::size_t n> void set(std::bitset<n>& bits, std::size_t i, nucleobase x) { switch (x) { case nucleobase::a: bits.set(i * 2, 0); bits.set(i * 2 + 1, 0); break; case nucleobase::c: bits.set(i * 2, 0); bits.set(i * 2 + 1, 1); break; case nucleobase::g: bits.set(i * 2, 1); bits.set(i * 2 + 1, 0); break; case nucleobase::t: bits.set(i * 2, 1); bits.set(i * 2 + 1, 1); break; } } template<std::size_t n> nucleobase get(const std::bitset<n>& bits, std::size_t i) { if (!bits[i * 2]) if (!bits[i * 2 + 1]) homecoming nucleobase::a; else homecoming nucleobase::c; else if (!bits[i * 2 + 1]) homecoming nucleobase::g; else homecoming nucleobase::t; }

live demo

the above illustration , terrible 1 (it's 4am here , need sleep).

for sec need map alleles , bits:

bit_pair bits_for(nucleobase x) { switch (x) { case nucleobase::a: homecoming bit_pair("00"); break; case nucleobase::c: homecoming bit_pair("10"); break; case nucleobase::g: homecoming bit_pair("01"); break; case nucleobase::t: homecoming bit_pair("11"); break; } } nucleobase nucleobase_for(bit_pair x) { switch (x.to_ulong()) { case 0: homecoming nucleobase::a; break; case 1: homecoming nucleobase::c; break; case 2: homecoming nucleobase::g; break; case 3: homecoming nucleobase::t; break; default: homecoming nucleobase::a; break; // warning } }

live demo

of course of study if need runtime length can utilize boost::dynamic_bitset , std::vector.

c++