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fix catalog links Adding atarva region files to allow STRchive loci to be genotyped with atarva Generate LongTR format STRchive catalog Generate STRanger catalog Change the way flanking motifs are described and handled (including schema update) Compatibility with STRanger annotation format Add Straglr catalog Update the atarva catalog to skip single motif flanking positions fix straglr catalogs to use STRchive ID instead of gene for all columns renamed basic bed files to .general.bed for consistency
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hdashnow
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Sep 5, 2025
## Description This PR will serve as a base for the changes coming in both #238 and #260. Fixes: #240 ## Major Changes - Reorder fields in schema and STRchive loci json to be more similar to locus pages - Automate sorting of STRchive loci json fields so that they match the schema order - Remove deprecated fields "type", "flank_motif" and "source" and where necessary integrate their content into other fields - Add new locus_structure format and check it against the reference genome for some unusual loci like FAME and XYLT1 ## Minor Changes - Fix citation in one of the ataxias that was pointing to the wrong disease ## Checklist - [x] All changes are well summarized - [x] Check all tests pass - [x] Check that the website preview looks good - [x] Update the STRchive version in `CITATION.cff`, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X. - [x] Ask someone to review this PR
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Any chance we can merge this sometime soon, or otherwise before #260? I have some entangled frontend changes that are in both PRs, and it'd be easier to merge this one first and then rebase #260 off of main afterward. I think you had said you didn't want to merge this one yet due to uncertainty in some of the data? Maybe we could just hide those particular data in the frontend for now? |
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Let me see if I can either fix and merge it, or at least merge most of it. |
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hdashnow
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Sep 9, 2025
## Description Adds catalogs for several new genotypers Replaces: #238 Should be merged before: #260 Related issues: #237 #185 #167 ## Major Changes - New genotyping and annotation catalogs: Atarva, LongTR, Straglr, Stranger - Improve look and functionality of catalog download table - Moved catalogs to `data/catalogs` subdirectory and renamed files for consistency - Change the way flanking motifs are described and handled (including schema update) ## Minor Changes - Minor edits to POLG and the FAME loci to improve catalog generation ## Checklist - [x] All changes are well summarized - [x] Check all tests pass - [x] Check that the website preview looks good - [x] Update the STRchive version in `CITATION.cff`, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X. - [x] Ask someone to review this PR --------- Co-authored-by: Vincent Rubinetti <vince.rubinetti@gmail.com>
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Description
Working on various catalog updates, see #237
Planning to collect #167 and #185 into this branch/PR before merging into main
Fixes: #237
Major Changes
Minor Changes
Checklist
CITATION.cff, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X.