Convert fasta file to 2-bit representation

2bit.cpp

#include <cassert>
#include <fstream>

struct cdata {
    uint64_t data;
    unsigned count;
    cdata() {reset();}
    void reset() {data = count = 0;}
    template<typename T>
    void write(T &stream, size_t nbytes=sizeof(data) / sizeof(char)) {
        stream.write((char *)&data, nbytes);
        reset();
    }
};

int main(int argc, char *argv[]) {
    if(argc < 2) {
        std::fprintf(stderr, "Usage: %s <infile> <outfile>\n", argv[0]);
        return EXIT_FAILURE;
    }
    std::ios_base::sync_with_stdio(false);
    std::ifstream ins(argv[1]);
    std::ofstream outs(argc > 2 ? argv[2]: "/dev/stdout", std::fstream::binary | std::ios::out);
    std::string line;
    cdata data;
    while(std::getline(ins, line)) {
        switch(line[0]) case '@': case '#': case '>': continue;
        for(const auto c: line) {
            switch(c) {
                case 'a': case 'A': break;
                case 'c': case 'C': data.data |= 1ull << 62; break;
                case 'g': case 'G': data.data |= 2ull << 62; break;
                case 't': case 'T': data.data |= 3ull << 62; break;
                default: continue;
            }
            if(++data.count == 32) data.write(outs);
            data.data >>= 2;
        }
    }
    data.data >>= (32 - data.count - 1) << 1;
    outs.write((char *)&data.data, (data.count >> 2) + ((data.count & 0x3u) != 0));
    return EXIT_SUCCESS;
}