Closed williamdlees closed 2 years ago
Thanks @williamdlees , I see change for the sphinx doc builds, but are there supposed to be field name changes? I see a commit but maybe the changes were already in master?
You are right, they do seem to be there, though I can't see from the change history how they got there from this branch. Perhaps it was something to do with the way you fixed up the changes I over-wrote?
needs more updates to germline.rst
@williamdlees I've added this branch to readthedocs so you can see the documentation changes.
I corrected the sentence, "In the case of a germline inference from a repertoire, ..." to refer to RearrangementSequence
instead of UnrearrangedSequence
. I think that is correct?
You may want to review the naming paragraph and add reference to you label generator tool. Also, the paragraph references coding_sequence_identifier
but it isn't in the schema. I'd filed #561 about that, is that field missing or has it been changed?
Thanks @schristley . Sorry I forgot to update the documentation. You are correct about that reference to RearrangedSequence instead of UnrearrangedSequence. coding_sequence_identifier has now disappeared: the approach we're suggesting now is that label should be the IUIS name or a temporary label. I've reflected that in the documentation and added a link to IgLabel.
I think everything should be ok now.
Some minor changes to germline field names for consistency, and a fix to conf.py which should stop the Sphinx build breaking: names of some of the schema elements needed updating.
closes #561 closes #560