HGVSnomenclature / hgvs-nomenclature

HGVS Nomenclature website
https://hgvs-nomenclature.org/
MIT License
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Remove "indel" except for where it's made clear it shouldn't be used. #145

Closed ifokkema closed 9 months ago

ifokkema commented 9 months ago

Replaced all mentions with "delins" except for in the hgvs package description; there, I changed the sentence to:

A key feature of the hgvs package is the ability to correctly project variants in the presence of genome-transcript alignment deletion/insertions (...)

@Reece, please change it if you prefer other wording.

Merging into 134-fix-all-remaining-style-issues to prevent lots of conflicts later, as that branch is changing all the lines that I'm editing now as well.

Closes #142.

ifokkema commented 9 months ago

@jfjlaros

In general, do we always use the term "deletion/insertion" in running text?

The site uses a combination of "deletion/insertion" and "deletion-insertion". Looking at the stats, the latter is actually more common. I guess it would be good if we would standardize this later as well.

@reece

LGTM too. Thanks for the cleanups and for asking about the hgvs block.

No worries! FYI: The general cleanup/styling is moving along slowly, but steadily.

jfjlaros commented 9 months ago

@ifokkema

I guess it would be good if we would standardize this later as well.

Agreed.

I also see we use the term delins in running text as well. I think it would be better to use common names (deletion, insertion, etc.) instead of operator names (del, ins, etc.) in running text.

ifokkema commented 9 months ago

@jfjlaros

I also see we use the term delins in running text as well. I think it would be better to use common names (deletion, insertion, etc.) instead of operator names (del, ins, etc.) in running text.

I agree. Currently, however, I'm working on a large update of every single page in the docs, and at least half of the lines (and often, more) are affected. So it would be great if we could do this only after I complete that work. Otherwise, I'll have to deal with a lot of conflicts. I'm also making a list of things that we should fix after I'm done.

jfjlaros commented 9 months ago

Sure, we can put it on our backlog.