multithreading bugfix; memory efficient string alleles for GWAS#212
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olivierlabayle merged 7 commits intomainfrom Feb 13, 2026
Merged
multithreading bugfix; memory efficient string alleles for GWAS#212olivierlabayle merged 7 commits intomainfrom
olivierlabayle merged 7 commits intomainfrom
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Could you add some tests to support the changes?
…(faster counting available in DataFrames.jl)
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@olivierlabayle Sorry about the tests. In thinking the change was straightforwards, in testing and experimentation I did find bugs 😆 Tests have been implemented and behavior is now expected with controls always being the major homozygous and the cases being the addition of the "alternate" allele based on dataset frequencies. Also found that StatsBase.jl's inclusion was completely unnecessary as there are faster level counting methods in DataFrames.jl. |
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@olivierlabayle Should be good to go here! |
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Thanks @joshua-slaughter!
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v 0.12.1
Fixes multithreading bug in building inputs in which there are less variants than threads. This can happen more frequently than expected if one has a sparse BED file or a large number of variants that do not pass QC.
Futhermore, we now utilise PooledArrays for the columns in the genotype dataset creation which matches the same memory burden as the former UInt8 implementation