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Change Genotype Dosage#4024

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lukasmueller merged 11 commits intomasterfrom
topic/change_genotype_dosage
Apr 29, 2022
Merged

Change Genotype Dosage#4024
lukasmueller merged 11 commits intomasterfrom
topic/change_genotype_dosage

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@nickmorales nickmorales commented Mar 28, 2022

Description

A db patch checks the saved genotyping protocols to see if the old dosage scheme was used, and then in a transaction updates the dosage for all stocks in those protocols.
On parsing of the genotyping data upload, the new dosage scheme is used.

closes #3906

Checklist

  • Refactoring only
  • Documentation only
  • Fixture update only
  • Bug fix
    • The relevant issue has been closed.
    • Further work is required.
  • New feature
    • Relevant tests have been created and run.
    • Data was added to the fixture
      • Data was added via a patch in /t/data/fixture/patches/.
    • User-Facing Change
      • The user manual in /docs has been updated.
    • Any new Perl has been documented using perldoc.
    • Any new JavaScript has been documented using JSDoc.
    • Any new legacy JavaScript has been moved from /js to /js/source/legacy.

@nickmorales nickmorales added the Priority: Do Not Merge PR should not be merged at the current time. label Mar 31, 2022
@nickmorales nickmorales removed the Priority: Do Not Merge PR should not be merged at the current time. label Apr 4, 2022
lukasmueller
lukasmueller approved these changes Apr 21, 2022
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:-)

@lukasmueller lukasmueller merged commit f9b89bd into master Apr 29, 2022
@lukasmueller lukasmueller deleted the topic/change_genotype_dosage branch April 29, 2022 18:00
@lukasmueller lukasmueller mentioned this pull request May 4, 2022
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@lukasmueller lukasmueller lukasmueller approved these changes

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Successfully merging this pull request may close these issues.

Allele dosages in VCFs count REF allele, _should_ count ALT to match header, marker-effects

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@nickmorales @lukasmueller