JoSS Review: Functionality about cerebra

[betteridiot]

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 it’s 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.

[lincoln-harris]

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.

[lincoln-harris]

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.