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Added dating and geographical information to .janno#317

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ltcrod merged 1 commit intoposeidon-framework:masterfrom
ltcrod:master
May 4, 2026
Merged

Added dating and geographical information to .janno#317
ltcrod merged 1 commit intoposeidon-framework:masterfrom
ltcrod:master

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@ltcrod
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@ltcrod ltcrod commented Mar 17, 2026

PR Checklist for modifying one or multiple existing packages

  • The changes maintain the structural integrity of the affected packages.
  • The checksums of the modified files in the respective POSEIDON.yml files were adjusted properly.
  • Every file in the submission is correctly referenced in the relevant POSEIDON.yml files and there are no additional, supplementary files in the submission that are not documented there.

  • The packageVersion numbers of the affected packages were increased in their POSEIDON.yml files.
  • The changes in the packageVersion followed the Poseidon Package versioning policy.
  • The changes were documented in the respective CHANGELOG files. If no CHANGELOG files existed previously it was added here.
  • The lastModified fields of the affected POSEIDON.yml files were updated.
  • The contributor fields were updated with name, email and orcid of the relevant, new contributors.
  • The .janno and the .ssf files are not fully quoted, so they only use single- or double quotes ("...", '...') to enclose text fields where it is strictly necessary (i.e. their entry includes a TAB).

  • All affected packages pass a validation with trident validate --fullGeno.

  • Large genotype data files are properly tracked with Git LFS and not directly pushed to the repository. For an instruction on how to set up Git LFS please look here. If you accidentally pushed the files the wrong way you can fix it with git lfs migrate import --no-rewrite path/to/file.bed (see here).

@ltcrod ltcrod merged commit 567aad1 into poseidon-framework:master May 4, 2026
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@nevrome
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nevrome commented May 4, 2026

For the sake of completeness: This PR was stuck for a long time, because @ltcrod got a genotype data parsing error with trident validate --fullGeno. This was caused by an incomplete clone (SMUDGE = 1). We investigated this together and cleared this PR.

Luca correctly remarked that All affected packages pass a validation with trident validate --fullGeno. and SMUDGE = 1 mutually exclude each other. But I think we don't require SMUDGE any more.

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2 participants