Add AIRR format import to tools

[Jason Vander Heiden]

We need to add the ability to use the AIRR format to DefineClones, AlignRecords and CreateGermlines.

Perhaps not for ParseDb and ConvertDb. We can assess how feasible and relevant that is later.

[Scott Christley]

I can help with this to some degree. At least in changes to the AIRR library as well as run tests on VDJServer.

[Jason Vander Heiden]

DefineClones is now working for AIRR format input and output.

[Jason Vander Heiden]

AlignRecords now has AIRR format I/O support.

[Jason Vander Heiden]

CreateGermlines is done.

Need to do ConvertDb, specifically for the genbank mode.

[Jason Vander Heiden]

ConvertDb-genbank is done.

For ConvertDb-fasta, ConvertDb-baseline, and all of ParseDb I don't think we need to have explicit support for the changeo or AIRR format. Those could all just be swapped to the python standard csv.writer because they don't actually require any content aware manipulation of the records. Just need to remove the case conversion of the headers.

[Jason Vander Heiden]

ConvertDb and ParseDb should now no longer care whether the input is changeo or airr formatted.

[Jason Vander Heiden]

Every tool now has AIRR support as of d699e7f.