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feat!: declare annotator CLI as console entrypoint#447

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jsstevenson merged 6 commits intomainfrom
vcf-script
Sep 5, 2024
Merged

feat!: declare annotator CLI as console entrypoint#447
jsstevenson merged 6 commits intomainfrom
vcf-script

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@jsstevenson jsstevenson commented Aug 30, 2024

Declare the annotator click function as a console entry point, enabling vrs-annotate input.vcf --vcf_out=out.vcf rather than python3 src/ga4gh/vrs/extras/vcf_annotation.py input.vcf --vcf_out=out.vcf.

Open to suggestions on the command name. I'd prefer a structure more along the lines of vrs-annotate vcf input.vcf --vcf_out=out.vcf (i.e., vrs-annotate is the command, vcf is a subcommand) if we think there's a chance that other filetypes could be annotated in the future (in that case, we may want to alter the module name as well). Alternatively, though, the subcommand might be superfluous if the file argument has a suffix indicating the filetype.

@jsstevenson jsstevenson marked this pull request as ready for review September 3, 2024 19:13
@jsstevenson jsstevenson requested review from a team as code owners September 3, 2024 19:13
@jsstevenson jsstevenson added the priority:low Low priority label Sep 3, 2024
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initial feelings seem to be supportive of vcf subcommand to vrs-annotate

@jsstevenson jsstevenson merged commit 36e8976 into main Sep 5, 2024
@jsstevenson jsstevenson deleted the vcf-script branch September 5, 2024 20:27
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