`constant` in rearragements spec should be treated as alignment-derived

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`constant` in rearragements spec should be treated as alignment-derived #22

Closed laserson closed 7 years ago

laserson commented 7 years ago

Mike Shugay pointed out that constant should be treated as an alignment-derived field, which it often is. We should probably rename to constant_call and add the associated fields (e.g., _score, _cigar). Any thoughts?

javh commented 7 years ago

Agreed. Maybe c_call? If we want to future proof, we could also add fields for the leader. I think MiXCR is the only aligner that currently calls the leader explicitly. I don't know if it distinguishes it from the V call though.