LOVD associated improvement requests and bugs

[John-F-Wagstaff]

This Issue exists as a meta-issue to coordinate both bug reports and feature requests associated with our friends at LOVD, i.e. mostly @ifokkema :-)

• Tools for handling variants with positions beyond the end of transcripts
  • Search by position Position based transcript search to be added to genes to transcript endpoint #582
  • Endpoint that returns within transcript positions for variants that exceed their span (this may need to be a new separate endpoint) Add mapping support for variants only partially intergenic #333
• User friendly web link for VV results Add a method to link to a validation result in the web interface #596
• Improved mitochondrial sequence/transcript support Support for missing chromosomal and "valid" model reference sequences #135

[John-F-Wagstaff]

We want to enable position based transcript search, via the API, mostly to find transcripts without hgvs valid descriptions for a variation span(span length exceeds transcript) that are nonetheless affected by said variation. #582

[John-F-Wagstaff]

We want to add the ability to directly link to the VV result for a specific variant via the user friendly web page (as opposed to the API). #596

[ifokkema]

Thanks, John!

I added a lot of issues in the past, but not all have to be added here. Some of them are just generic, and others can be worked around or simply aren't that important. We could also add a specific label to GitHub for LOVD-related requests? I could then label the most important issues, and we'll be able to quickly filter for them.

Otherwise, if we want to keep things here, that's also fine. I can't edit this issue, so I'll add some comments here below. Could you update the issue text?

• For Position based transcript search to be added to genes to transcript endpoint #582, it is essential that I have some form of position of the transcript so I can calculate the overlap. E.g., that I would be able to know that the deletion spans from, e.g., c.1000 to c.*1000 (even if the latter doesn't exist), or that I would get position and breakpoint annotation, e.g., input deletion is g.100000_200000 and the output indicates that the transcript lies at 150000 to 250000 and that 200000 (deletion end) corresponds to c.1000. That way, I will be able to generate my own HGVS (or HGVS-like) descriptions.
• Please add Support for missing chromosomal and "valid" model reference sequences #135 as a requirement as well; Mutalyzer created a workaround for us forever ago to handle mitochondrial genes, and I would like to keep support for mitochondrial genes in LOVD3, but then using VV.

[ifokkema]

Also related to #582, with more examples, is #333.

[John-F-Wagstaff]

I assume that this is mostly for storing and organising the high priory issues, so that we can organise a road map, and coordinate priorities with you, as well as focusing on what you need next. I just made this at request though so @Peter-J-Freeman can correct me if I got this wrong.

[Peter-J-Freeman]

Exactly @John-F-Wagstaff . Want to create the roadmap and sort now that I also have dev time

[John-F-Wagstaff]

Unfortunately I can't see a way to give you edit access to the initial comment. As such if you want to make changes to the task list you either need to post them and ask me to make them, or have me step back, by editing a comment that you own in the thread to replace the original, and asking me to remove the to-do/priority list from the first one.

[ifokkema]

@John-F-Wagstaff No worries! I think the current list is definitely the top list 😁