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 -s and 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.
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