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Investigate performance implications of using Java serialization for genotypes #55

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heuermh opened this issue Oct 24, 2018 · 1 comment
Open

Investigate performance implications of using Java serialization for genotypes #55

heuermh opened this issue Oct 24, 2018 · 1 comment

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@heuermh
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heuermh commented Oct 24, 2018

Pull request #52 uses JavaSerializer for htsjdk.variant.variantcontext.LazyGenotypesContext to workaround issues with serializing transient fields.

Java binary serialization is demonstratively worse than Kryo, in both read/write speed and size in memory, so we should follow up with an investigation of how much this matters for performance in Disq for genotypes. Other options might include: modify LazyGenotypesContext so that it can be serialized by Kryo, write a custom Kryo serializer for LazyGenotypesContext, etc.
@heuermh
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heuermh commented Feb 23, 2021 •
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Worth revisiting this to see if still an issue with the latest htsjdk.

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