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Rechunk dosages so there is no chunking in the samples dimension #35

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tomwhite opened this issue Mar 31, 2021 · 0 comments
Open

Rechunk dosages so there is no chunking in the samples dimension #35

tomwhite opened this issue Mar 31, 2021 · 0 comments

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@tomwhite
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This is one of the key findings from https://github.com/pystatgen/sgkit/issues/390#issuecomment-781503522.

More detail at https://github.com/pystatgen/sgkit/issues/448#issuecomment-780655217. We should rechunk the dosages array (using rechunker), so that chunk sizes are {variant: 64, sample: -1}. (The -1 means no chunking in the samples dimension.)

Note that this should be done as a separate rechunking step, and not as a part of the run_gwas function in gwas.py since the latter will rechunk for each trait group.

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