Initial tskit conversion code #346
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| self.num_records = self.ts.num_sites | ||
| self.positions = self.ts.sites_position | ||
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| def _make_sample_mapping(self, ploidy): |
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This feels like it belongs in tskit. Let's file an issue there to support once we have something working committed here.
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| def iter_field(self, field_name, shape, start, stop): | ||
| if field_name == "position": | ||
| for pos in self.ts.tables.sites.position[start:stop]: |
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self.ts.sites_position - you're creating a copy of the tables every time here!
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| self.samples = [vcz.Sample(id=f"tsk_{j}") for j in range(self.num_samples)] | ||
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| def iter_alleles(self, start, stop, num_alleles): |
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Ah yes, it's a bit unfortunate we have to do this. I can see ways to work around though.
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Stacked on #344, clean diff at 9f5ae9a