Fix partner variant bug #486
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| self.pedigree.by_id[sample_id].affected != '2' | ||
| or not principal.sample_category_check(sample_id, allow_support=False) |
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none of this ended up being relevant, but it makes the logic easier to read
| # thin out the possible partners by alt depth | ||
| return [ | ||
| var | ||
| for var in comp_hets[sample].get(first_variant, []) | ||
| if not var.check_minimum_alt_depth(sample, min_alt_depth) | ||
| ] |
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I think this was the issue - I was getting a Bool value for if the current variant was support-only, then using that to decide if a partner could also be support-only. It was a mess of booleans, so I've dropped it from here completely. Once we find all the partners, there's a simpler test on each pair that at least one must be non-support.
| return [ | ||
| var | ||
| for var in comp_hets[sample].get(first_variant, []) | ||
| if not var.check_minimum_alt_depth(sample, min_alt_depth) |
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I know it is not part of this PR, but the check_minimum_alt_depth method name is a bit curly (ie the not in front of it confused me)
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Yup, I think I should revisit all the method names to optimise the logic they're involved in...
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