Comments (3)
Since it is a boolean, maybe setting up click
to use a flag instead would be a more intuitive approach:
Boolean flags are options that can be enabled or disabled. This can be accomplished by defining two flags in one go separated > by a slash (/) for enabling or disabling the option. (If a slash is in an option string, Click automatically knows that itβs a boolean > flag and will pass
is_flag=True
implicitly.) Click always wants you to provide an enable and disable flag so that you can change > the default later.
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RE point 3 and this cryptic error message:
<class 'hgvs.edit.AASub'> <class 'hgvs.edit.AARefAlt'>
your right, this was an error message meant for internal debugging.
shouldnt be seeing it anymore.
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2 and 4 should be addressed by the latest PR. basically the report-coverage
option for find-peptide-variants
returns a string that gives you some idea of the reads support for a given variant call. for example the string:
'ENSP00000395243.3:p.(Leu813delinsArgTrp),[2:0]'
tells you you have the ENSP00000395243.3 variant with an insertion of ArgTrp in place of Leu at position 813. At this loci we find 2 variant reads and 0 wildtype
This option is indeed a boolean; I hope I've made that more clear in USAGE.md of the new PR.
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Related Issues (20)
- zlib error HOT 2
- vcfpy exception HOT 2
- JoSS Review: Installation HOT 5
- JoSS Review: Automated Tests
- JoSS Review: Community Guidelines
- count-variants not runnable without specifying cosmicdb HOT 1
- Versioning question
- Requirements and CI
- Python 3.8 support
- Universal wheel
- Review comments on CONTRIBUTING.md HOT 6
- Installation process HOT 8
- improve testing speed HOT 3
- pysam build fails on python3.8 HOT 5
- JoSS Review: Clarify README.md HOT 3
- JoSS Review: Quality of writing HOT 3
- trouble adding to bioconda
- would like to make cerebra modules importable
- hgvs throwing stdout
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