Finding the memory allocation in some code

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4

I believe $GeneticVariation.DEFAULT_TRANS should be $(GeneticVariation.DEFAULT_TRANS). You’re interpolating the module, but not the constant. This makes the allocations go away in both functions.

My test code:

using BioSequences
using BioSequences.GeneticCode
using GeneticVariation
using BenchmarkTools

const CDN = Union{BioSequences.DNACodon, BioSequences.RNACodon}
const DEFAULT_TRANS = BioSequences.ncbi_trans_table[1]
const CDN_POS_MASKS = (0xFFFFFFFFFFFFFFFC, 0xFFFFFFFFFFFFFFF3, 0xFFFFFFFFFFFFFFCF)


function expected_NG86_min(codon::C, k::Float64, code::GeneticCode) where {C <: CDN}
    cdn_bits = UInt64(codon)
    S = N = 0.0
    for (pos, msk) in enumerate(CDN_POS_MASKS)
        @inbounds for base in 0:3
            # Create the neighbor codon.
            ins = base << (2 * (pos - 1))
            neighbor = C((cdn_bits & msk) | ins)
            S += 1.0
            N += 1.0
        end
    end
    normalization = (N + S) / 3
    return (S / normalization), (N / normalization)
end

cdn = DNACodon(0x000000000000000) # a test codon to benchmark and look at allocation.

@benchmark expected_NG86_min($cdn, 1.0, $(GeneticVariation.DEFAULT_TRANS))
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