Locus matching: tagged loci, composite rows, exact preference - #23
Merged
Merged
Conversation
- The gene rule strips a feature-type tag from a coordinate and keeps the rest whole: chr1:0-100_Peaks matches chr1:0-100 again; Mixed keys it as 1:0-100. - GeneIndex finds a row's locus part (whole name, '/'-core, or the locus of an id_name join such as chr1:100-200_GENE1). A locus query matches the same name first, then locus key plus rest, then a bare key; a whole-locus row wins its key over one that only starts with it. - h5ad feature types are read from var/feature_type or var/feature_types (scanpy, muon). - The non-colon warning fires at a tenth of the axis, and also when an explicit overlap kind finds no colon loci; an untyped list that only partly reads as intervals is logged; the import count is rows. Requires legume-genomic-types 0.5.3. Release 0.7.2.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Review follow-ups to the strict colon rule (these were meant for 0.7.1 but missed its merge).
chr1:0-100_Peaksmatcheschr1:0-100again;Mixedkeys it as1:0-100.GeneIndexfinds a row's locus part (whole name,/-core, or the locus of anid_namejoin such aschr1:100-200_GENE1). A locus query matches the same name first, then locus key plus rest, then a bare key; a whole-locus row wins its key over one that only starts with it.var/feature_typeorvar/feature_types(scanpy, muon), so mixed files get their peaks converted.Requires legume-genomic-types 0.5.3. Version 0.7.2.