feat: implement alignment param presets #1569
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ivan-aksamentov
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Feb 21, 2025
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| pub fn from_preset(preset_name: impl AsRef<str>) -> Result<AlignPairwiseParams, Report> { | ||
| let preset_name = preset_name.as_ref(); | ||
| match preset_name { | ||
| "default" => Ok(AlignPairwiseParams::default()), | ||
| "high-diversity" => Ok(AlignPairwiseParams { | ||
| alignment_preset: o!("high-diversity"), | ||
| penalty_gap_extend: 0, | ||
| penalty_gap_open: 999999, // FIXME: dummy values | ||
| penalty_gap_open_in_frame: 88888, // FIXME: dummy values | ||
| penalty_gap_open_out_of_frame: 77777, // FIXME: dummy values | ||
| penalty_mismatch: 6666, // FIXME: dummy values | ||
| score_match: 33333, // FIXME: dummy values | ||
| ..AlignPairwiseParams::default() | ||
| }), | ||
| "short-sequences" => Ok(AlignPairwiseParams { | ||
| alignment_preset: o!("short-sequences"), | ||
| min_length: 0, // FIXME: dummy values | ||
| ..AlignPairwiseParams::default() | ||
| }), | ||
| _ => make_error!("Alignment params preset not found: {preset_name}"), | ||
| } | ||
| } |
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The presets are defined here.
These are the dummy values to be tweaked.
ivan-aksamentov
commented
Feb 21, 2025
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| /// Alignment param preset | ||
| #[clap(long, default_value = ALIGNMENT_PRESET_DEFAULT)] | ||
| pub alignment_preset: String, |
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CLI arg help text needs to be adjusted
Define some hard-coded presets of alignment parameters additionally to the default one. The `--alignment-preset` arg allows users to toggle between presets. Example: ```bash nextclade run --dataset-name=sars-cov-2 -O tmp/sars-cov-2 sequences.fasta --alignment-preset=high-diversity --verbosity=info ```
ivan-aksamentov
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Nice stuff! @anna-parker you might be interested in this one potentially 😀 |
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Define some hard-coded presets of alignment parameters additionally to the default one.
The
--alignment-presetarg allows users to toggle between presets.Example: