Verify indexing for functions

[Jason Vander Heiden]

Need a careful check for the indexing scheme everywhere.

In particular, verify whether Parsers.padAlignment takes 0-based or 1-based indexes.

Indexes are stored in Receptor.Receptor are currently 1-based closed intervals like the IgBLAST and IMGT/HighV-QUEST, but we probably want to swap this to 0-based open intervals like native python and the AIRR standard.

That'll be tedious, but... I think it needs doing.

[Jason Vander Heiden]

Parsers.padAlignment is 0-based indexing.

[Jason Vander Heiden]

Some inconsistency still, but it's documented. Will wait on any airr standard changes before modifying.