Api suggestion #90
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Api suggestion #90
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| for key, intervals in self.interval_fetcher: | ||
| intervals.sort(key=lambda x: x.start) | ||
| # Fetch variants corresponding to the intervals | ||
| intervals_with_variants = [(interval, self.variant_source.fetch_variants(interval)) |
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This is a very slow way to match variants. A better approach will be overlapping with pyranges if the variant strategy is single variant.
https://github.com/kipoi/kipoiseq/blob/master/kipoiseq/extractors/vcf_matching.py#L148
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As general, those classes are a good idea. They combine small building block extractors into dataloader in a generic way. |
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