Exclude samples #80
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Exclude samples #80
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tomwhite
reviewed
Sep 11, 2024
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Thanks for working on this @Will-Tyler.
bcftools view lets the user simultaneously include samples with
-sand exclude samples with-S. I think the expected behavior in different cases (e.g. a sample that is both included and excluded) is not well-defined, so vcztools just throws an assertion error in this implementation. I can try to copy bcftools view's behavior if desired or open a separate issue to track this.
I think it is OK to raise an error in this case. If we want to match bcftools behaviour in the future then we can.
Can you add a test for this case please (failing if both -s and -S are specified)?
tomwhite
approved these changes
Sep 13, 2024
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Overview
The bcftools view CLI allows users to exclude samples from the output with the
^character. This pull request makes vcztools view do the same.This pull request closes #74.
Testing
I had some unit and validation tests.
Discussion
bcftools view lets the user simultaneously include samples with
-sand exclude samples with-S. I think the expected behavior in different cases (e.g. a sample that is both included and excluded) is not well-defined, so vcztools just throws an assertion error in this implementation. I can try to copy bcftools view's behavior if desired or open a separate issue to track this.References