Improve error reporting

[Jason Vander Heiden]

Errors can be ambiguous in cases where columns are missing or records have been failed due to internal checks. We need to do a pass through all the error/warning reports and add column checks.

Some issues currently:

• CreateGermlines will fail sequences with a length mismatch if the NP1_LENGTH and NP2_LENGTH are missing, because they default to 0 if absent. We should pre-check to make sure these are present and exit if they're not.
• MakeDb doesn't have a log file, so it's unclear when a sequence is failed because the JUNCTION and SEQUENCE_IMGT values don't align properly.
• MakeDb reports missing germlines to stderr instead of a log.
• MakeDb and CreateGermlines will fail without IMGT-gapped germlines, but we don't pre-check that the reference set is properly IMGT-gapped, so the basis for failure is unclear. It may be sufficient to check for dots in the reference set - otherwise, I'm not sure how we would about this without engineering a way to gap germlines de novo.

[Jason Vander Heiden]

We could probably do an error only log file for MakeDb. It would be a little weird, because nothing else works like that, but probably better than dumping every error to stderr.

[Jason Vander Heiden]

• Added check for missing fields to CreateGermlines and ConvertDb-genbank.
• Added naive check for IMGT-gapped references in CreateGermlines and MakeDB.

[Jason Vander Heiden]

Getting MakeDb messages into a log is going to require some restructuring of IO.IMGTReader, IO.IgBLASTReader and IO.IHMMuneReader. Probably the easiest way is to add a log handle argument to each, add exception raises with informative messages during parser errors in the relevant functions/methods, and have the reader catch those execeptions and write the log as it iterates independent of MakeDb's writer.

[Jason Vander Heiden]

Added the --log argument to MakeDb in 5a2125e. Going to skip dumping missing germline messages into the log. It's a lot of work, and it might actually be better for the warning to be "in your face" more so you fix it.