Use of the germline set, and error when it is provided

[williamdlees]

Attaching a germline set gave me the error 'Warning: Error in [: subscript out of bounds'. and the analysis stopped without providing a report.

Perhaps this is because the germline set did not include some alleled referenced in the file? The tool should continue in this circumstance, and provide a suitable report at the end.

It's not clear to me why a germline set is needed - the reason given is to provide germline usage statistics, but can the tool not wor out what alleles have been used from the values in the columns?

Finally there should be some guidance on what is required: for example should V-genes be gapped, is the set expected to cover V, D and J?