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Behaviour of a Filterable object #4
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I think it is important that if no filters are set then all the variants
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Can't be important - not been an issue, might have fxed it. Dunno really. |
Since issue #2 the VcfWriter so output is now more compatible with the actual VCF spec, in particular, if a variant has not been filtered the FILTER column should be empty for that variant:
However this has raised a question about the Filterable interface which I'd like some feedback on as it impacts a fundamental behaviour. Currently a Filterable either passes or fails, but really it can exist in one of three states - passed, failed and unfiltered/not yet filtered. Given this:
It would be possible to keep the existing behaviour of passedFilters and add getFilterStatus for ease of use and backwards compatibility at the expense of some potential confusion. But this all depends on what people are using - will any of these changes actually have any direct impact on you? If not I suggest clean logic should be applied as this tends to keeps things simpler and simple is good.
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