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feat: add --chunk-size parameter to simgenotype and fix RuntimeError when reference coordinates extend past the final map file coordinate #268

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merged 22 commits into from
Jan 3, 2025

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@aryarm aryarm commented Dec 20, 2024

Resolves #267

Allows for writing PGEN files while using less memory via a new --chunk-size parameter. Also fixes a RuntimeError that would arise when the coordinate of a variant in the reference was greater than the final coordinate in the input .map file.

@aryarm aryarm requested a review from mlamkin7 December 20, 2024 16:48
@aryarm aryarm marked this pull request as draft December 30, 2024 03:47
@mlamkin7 mlamkin7 marked this pull request as ready for review December 30, 2024 06:18
@mlamkin7 mlamkin7 self-requested a review December 30, 2024 06:19
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@aryarm not sure how to add you as a reviewer but would you be able to check my work?

@aryarm aryarm changed the title feat: add --chunk-size parameter to simgenotype feat: add --chunk-size parameter to simgenotype and fix RuntimeError when reference coordinates extend past the final map file coordinate Dec 30, 2024
@aryarm aryarm merged commit 4c22846 into main Jan 3, 2025
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@aryarm aryarm deleted the feat/chunk-simgts branch January 3, 2025 15:43
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RuntimeError: append_alleles_batch
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