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Adding all the last G2P fixes to 113#780

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dglemos merged 2 commits intoEnsembl:release/113from
olaaustine:all_g2p_changes
Mar 17, 2025
Merged

Adding all the last G2P fixes to 113#780
dglemos merged 2 commits intoEnsembl:release/113from
olaaustine:all_g2p_changes

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@olaaustine olaaustine commented Mar 11, 2025

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@olaaustine olaaustine requested a review from dglemos March 11, 2025 11:21
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dglemos commented Mar 11, 2025

This change is already merged into release/114 and main, now we only want to add it to release/113.
Can you update the PR base branch to release/113? Also, at this point in the release we don't use postreleasefix/113 anymore.

For reference, this PR includes changes from #777 into release/113.

@olaaustine olaaustine changed the base branch from postreleasefix/113 to release/113 March 11, 2025 15:56
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olaaustine commented Mar 11, 2025

This change is already merged into release/114 and main, now we only want to add it to release/113. Can you update the PR base branch to release/113? Also, at this point in the release we don't use postreleasefix/113 anymore.

For reference, this PR includes changes from #777 into release/113.

It also has changes from #770

dglemos
dglemos reviewed Mar 17, 2025
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G2P.pm
* 'gnomADe' & 'gnomADe_r2.1.1 & 'gnomADev4.1' - gnomADe:AFR, gnomADe:ALL, gnomADe:AMR, gnomADe:ASJ, gnomADe:EAS, gnomADe:FIN, gnomADe:NFE, gnomADe:OTH, gnomADe:SAS (for GRCh37 and GRCh38 respectively).
* 'gnomADg' & 'gnomADg_v3.1.2' & 'gnomADgv4.1' - gnomADg:AFR, gnomADg:ALL, gnomADg:AMR, gnomADg:ASJ, gnomADg:EAS, gnomADg:FIN, gnomADg:NFE, gnomADg:OTH (for GRCh37 and GRCh38 respectively).
Need to use 'af_from_vcf' parameter to use this option.
default_af : default frequency of the input variant if no frequency data is
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The option 'default_af' was not removed in #770 or #777
As this PR is only going to be available for release/113 there is no point to remove the option here.

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@olaaustine olaaustine Mar 17, 2025

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I added this because I wanted us to remove it from the Perldoc, I will also make a mini PR for 114, thats the plan.

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Yes, the plan is for future releases.

@dglemos dglemos merged commit 1005408 into Ensembl:release/113 Mar 17, 2025
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