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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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transcript select for mane and pick in split-vep #2071

Closed barslmn closed 6 months ago

barslmn commented 6 months ago

I copy-pasted from the CANONICAL selection. Only difference is with matching the mane transcript where there is additional function call to strncpy for matching "NM".

pd3 commented 6 months ago

Thank you for the pull request. Before it can be considered, the test suite must pass and tests for the new functionality added.

barslmn commented 6 months ago

Hi, tests are passing.

This functionality does depend on the vep command being used having the --pick parameter. As well as the reference genome since hg19 wont have the mane select.

pd3 commented 6 months ago

Thank you, it looks good at a brief glance. It will still need a test case before it can be merged.

barslmn commented 6 months ago

I can supply test cases and write the tests. Would you direct me where do I put these tests or any guidelines? I only see the data files under test/ dir.

pd3 commented 6 months ago

Actually, don't worry about it, I will add the tests myself. I just got a similar request and realized it will be better to turn this into something more general, based on regular expressions. I will do that, adding your 'pick' and 'mane' functionality as presets.

barslmn commented 6 months ago

Thanks a lot

pd3 commented 6 months ago

This has been now implemented in https://github.com/samtools/bcftools/commit/944fc9339f441f25c879170aaa7dc530e55d7d9b