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perf: Add bounds for haplotype matrix #61

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Dec 22, 2023
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perf: Add bounds for haplotype matrix #61

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4928e71
perf: Add bounds for haplotype matrix
MillironX Dec 21, 2023
b0129a7
chore: Update CHANGELOG
MillironX Dec 22, 2023
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perf: Add bounds for haplotype matrix 
We know that the upper bound for the value of any cell in the occurence
matrix has to be equal to or less than the number of reads. Leverage that
knowledge to shrink the size of arrays that are needed.
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@MillironX
MillironX committed Dec 22, 2023
commit 4928e714c9a99a3bb67c87669ae207b47ddf641e
11 changes: 10 additions & 1 deletion src/haplotypecalling.jl
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Expand Up @@ -253,7 +253,16 @@ dimensional matrix.
function occurrence_matrix(
haplotype::AbstractArray{Variation{S,T}}, reads::AbstractArray{Haplotype{S,T}}
) where {S<:BioSequence,T<:BioSymbol}
hapcounts = SparseArray{UInt}(undef, Tuple(repeat([2], length(haplotype))))
Q = UInt
for int_type in [UInt8, UInt16, UInt32, UInt64, UInt128]
if length(reads) < typemax(int_type)
Q = int_type
break
end #if
error("Too many reads to represent in memory")
end #for

hapcounts = SparseArray{Q}(undef, Tuple(repeat([2], length(haplotype))))

for read in reads
coordinates = zeros(Int, size(haplotype))
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