Super neat JS work! I have similar code for doing GC/AT counts in java. Using longs and popcount one can do 16 nucleotide per cycle. Also what is nice is that one can easily use a memory mapped byte buffer as long buffer to run through the code. To go faster than that AVX needs to be used/jitted in.
What it really shows is that the FASTA format is just terrible for computational efficiency :(
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Super neat JS work! I have similar code for doing GC/AT counts in java. Using longs and popcount one can do 16 nucleotide per cycle. Also what is nice is that one can easily use a memory mapped byte buffer as long buffer to run through the code. To go faster than that AVX needs to be used/jitted in.
What it really shows is that the FASTA format is just terrible for computational efficiency :(
https://gist.github.com/JervenBolleman/d1430d0549028861504c