feat: set gap alignment to "left" by default #1377
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Not blocking but it would be nice if we could indicate the default value in the CLI help. Right now it says "possible values left, right" but not which one is the default. |
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@corneliusroemer I made it as follows now: |
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This text could be incorrect though depending on how dataset is configured, which we have no way of telling at the time of printing help text. |
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Thanks, that's great! I think it's ok that pathogen json can overrides default and CLI won't show. The CLI just shows the bare default that applies in case nothing overrides. |
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@corneliusroemer We have a failing test now. Can you help me with it? |
The unit test `pads_missing_left()` is failing: https://github.com/nextstrain/nextclade/blob/cc9e817b2195ccc39c1094800857f512ed6ad82f/packages_rs/nextclade/src/align/score_matrix.rs#L241-L294 with this error: https://github.com/nextstrain/nextclade/actions/runs/7477824073/job/20351461502?pr=1377#step:7:398 Probably due to retying on the previous default value of the "gap alignment side" parameter ("right"). So I decided to make 2 tests instead of this one: - `pads_missing_left()` using the default "left" value for "gap alignment side" now got the new expectations. I copied them from the actual result, so they need to be scientifically checked. - `pads_missing_left_with_alignment_gap_right()` retained previous expectations, but is now using "right" in the "gap alignment side". Both tests are passing, but the expectations for the `pads_missing_left()` need to be checked by hand.
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The validating the path matrices is a bit tricky, but it all looks correct to me. |
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