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* Variants are now stored in a set, not a list. The VariantCollection constructor can take any iterable of variants and will convert it to a set. * The `__str__` method now gives a short summary with just the variant count. The original `__str__` method, which gives a line for each variant, has been moved into the `variant_summary` method. * The `reference_names` and `gene_counts` methods have been converted to memoized properties.
* Remove VariantCollection.drop_duplicates since variants are now stored in a set. * Make Variant instances comparable. They are ordered by locus. * Update tests
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I'm not sure about dropping this test entirely, we still probably want to ensure that the expect behavior happens when you initialize a variant collection with duplicates (though now that expected behavior is just the second assert below).
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Other than (1) adding a test which explicitly expects dropping duplicates by default and (2) moving |
Also update tests, and add a test that variant collections do not include duplicate variants.
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__str__method now gives a short summary with just the variant count. The original__str__method, which gives a line for each variant, has been moved into thevariant_summarymethod.reference_namesandgene_countsmethods have been converted to memoized properties.