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[I/O] Update VCF -> cuDF parser with more optimized version #135

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tijyojwad opened this issue Oct 19, 2020 · 0 comments
Open

[I/O] Update VCF -> cuDF parser with more optimized version #135

tijyojwad opened this issue Oct 19, 2020 · 0 comments
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@tijyojwad
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The current VCFReader implementation depends on cyvcf2 to parse the underlying file, and then converts each row into a data frame array. However, this is fairly slow. For vcfio to be more useful in VCF annotation flows, the parser needs to be ~5x faster than it is currently.

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