feat: deprecate old alignment params #1270
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ivan-aksamentov
commented
Oct 11, 2023
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| (o!("--min-seeds (minSeeds)"), &self.min_seeds), | ||
| (o!("--seed-length (seedLength)"), &self.seed_length), | ||
| (o!("--seed-spacing (seedSpacing)"), &self.seed_spacing), | ||
| (o!("--min-match-rate (minMatchRate)"), &self.min_match_rate), | ||
| (o!("--mismatches-allowed (mismatchesAllowed)"), &self.mismatches_allowed), | ||
| (o!("--max-indel (maxIndel)"), &self.max_indel), |
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These are the params being deprecated.
And the error message is constructed just below this fragment.
Let's use `kmer_length` instead of removed `seed_length` and adjust the coefficient to roughly match the old value.
ivan-aksamentov
commented
Oct 12, 2023
| @@ -46,7 +46,7 @@ pub fn align_nuc( | |||
| ); | |||
| } | |||
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| if ref_len + qry_len < (10 * params.seed_length) { | |||
| if ref_len + qry_len < (20 * params.kmer_length) { | |||
| // for very short sequences, use full square | |||
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According to Richard's recommendation, for short sequence check let's use kmer_length instead of removed seed_length and adjust the coefficient to roughly match the old value.
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Here I deprecate some of the alignment params which lost their use after the alignment algo was changed.
I emit an error if any of these parameters are still present in CLI args and/or in dataset's
pathogen.json. We could also make it a warning.