docs(lapis-docs): add documentation for interaction between 'maybe' and 'not'#1591
docs(lapis-docs): add documentation for interaction between 'maybe' and 'not'#1591
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Pull request overview
Adds clarification to LAPIS documentation about how ambiguous symbols interact with negation, addressing confusion raised in issue #1554 (e.g., why NOT A134C/!A134C can match sequences with ambiguous/unknown bases at that position).
Changes:
- Extend the “Ambiguous symbols” concept doc with a new section explaining
MAYBEvs negation. - Provide a small example demonstrating the difference between
!3Gand!MAYBE(3G).
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| ### `MAYBE` and `NOT` | ||
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| Ambiguous symbols and negation (`not` or `!`) can sometimes seem a bit unintuitive. | ||
| When querying for sequences that do _not_ have - for example - a G at position 3, should that include ambiguous sequences or not? |
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In this doc page the query language is described as (variant) query syntax, where negation is written as !. Referring to negation as not here can be confusing because not isn't part of the variant-query grammar; consider referencing NOT (advanced query keyword) and/or explicitly stating which of NOT/! applies to which query language.
| ### `MAYBE` and `NOT` | |
| Ambiguous symbols and negation (`not` or `!`) can sometimes seem a bit unintuitive. | |
| When querying for sequences that do _not_ have - for example - a G at position 3, should that include ambiguous sequences or not? | |
| ### `MAYBE` and negation | |
| Ambiguous symbols and negation (written as `!` in variant queries) can sometimes seem a bit unintuitive. (In the advanced query language, the equivalent keyword is `NOT`.) | |
| When querying for sequences that do not contain—for example—a G at position 3, should that include ambiguous sequences or not? |
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Is this correct? Did I just mix up variant and advanced queries, @fengelniederhammer ?
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No, I think you are correct. IMO we don't need to document variant queries that much, because they are for Covid only.
But we should somehow say "in advanced queries", because "not" only exists there. The normal mutation filters allow maybe, but not not.
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And yes, I think not does not exist in variant queries. But that's neglectable.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
resolves #1554
PR Checklist
All necessary changes are explained in thellms.txt.The implemented feature is covered by an appropriate test.