Add output option to vcztools view #66
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Should we check that the filename has a .vcf suffix? Bcftools will use the suffix to detect the output type, and since we only support uncompressed VCF, it might be a good idea to fail if the user tries to write to a .vcf.gz or .bcf file for example.
tests/test_cli.py
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| output = tmp_path / "output.vcf" | ||
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| run_vcztools(f"view {vcz_path} --output {output}") | ||
| assert os.path.exists(output) |
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Can you call assert_vcfs_close to check the output is correct?
Also, perhaps this should belong in test_bcftools_validation as you are using run_vcztools from there anyway?
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Failing loudly when we can't do something (or if we depart from bcftools behaviour) should be a basic guiding principle for us I think, so I like @tomwhite's suggestion above. It is a separate issue though, so we could just log an issue to track and do in a follow-up. |
Overview
This pull request adds an
-o / --outputoption to thevcztools viewCLI. The option allows the user to specify a file to write the CLI output to.This pull request closes #54.
Testing
I add a unit test that writes a file using the output option and confirms that the file is present.
References