IMGT seqence/germline build in ConvertDb doesn't seem right
Look into the behavior of the -r
argument to ConvertDb-airr and ConvertDb-changeo. It doesn't seem correct, at a glance.
Comments (5)
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reporter -
reporter Schedule for v0.4.3.
And maybe move it out of ConvertDb-changeo and ConvertDb-airr into a separate subcommand. It's kind of clunky to trying to combine the gapping with flexible (airr -> airr and airr -> changeo) I/O.
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reporter Maybe it would be better to make this a MakeDb-airr command, given the decision to switch the core format to the AIRR standard. The basic functionality would be to take in an AIRR Rearrangement file and do a little standardization within that scope. For now, I see this only entailing:
- Adding IMGT gaps to
sequence_alignment
andgermline_alignment
and modifying the appropriate germline start/end fields. - Redefining
productive
andjunction_aa
based on thejunction
frame. - Filling in positional fields required by CreateGermlines from the
_cigar
fields. - Add the
locus
field if needed.
All as options, because the input AIRR file could come from any source, not just IgBLAST.
- Adding IMGT gaps to
-
Is this mainly dealing with different fields names, or does new functionality need to be written? I would also vote for the IMGT gapped alignments to be put in new fields instead of overwriting the existing field content.
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reporter Some new functionality is needed, which is why it’s taking me so long to get around to it. The bottleneck testing the existing IMGT-gapping methods on different outputs. The field renaming stuff and conversion from
_length
to_end
is all already in ConvertDb. - Log in to comment
May be best to simply exclude the
-r
functionality from the 0.4.1 release.