Use AIRR-ish names for output fields of calcJunctionAlignment

[Jason Vander Heiden]

I seem to recall us tossing around some reserved field names for 3' and 5' deletion fields in the AIRR schema once upon a time - in the context of partis. Might make sense to use those field names or something similar. I can’t recall exactly, but I think it was something like:

• d3v_length
• d5d_length
• d3d_length
• d5j_length

Ie, the prefix is n for untemplated insertion, p for palindromic insertions, and d for deletions. Or something like that.

Also, calcJunctionAlignment seems a bit wordy for alakazam. Maybe junctionAlignment. Not really import though.

[ssnn]

I renamed calcJunctionAlignment to junctionAlignment

I didn’t find dv3_length or the other field names in the AIRR-C repo issue tracker. I did find a thread where you suggested to include this information, but I guess it wasn’t (https://github.com/airr-community/airr-standards/issues/139).

I think it will be best to move this conversation/decision to the AIRR-C repo, so we have a community field name.

[ssnn]

Renamed calcJjunctionAlignment fields

See issue 96 for details https://bitbucket.org/kleinstein/alakazam/issues/96/use-airr-ish-names-for-output-fields-of

→ <<cset 4352c94e349b>>

[ssnn]

#4352c94