CreateGermlines --cloned: select one D using majority rule

[ssnn]

Currently, CreateGermlines --cloned uses a majority rule to select one V and one J to be used to create one germline per clone. The first D is selected.

https://bitbucket.org/kleinstein/changeo/src/017f7a65519b7c214d8aae786d7bee0069e2cd27/changeo/Gene.py#lines-384:386

We need to test if applying the majority rule to D will cause losing many sequences in the next steps:

https://bitbucket.org/kleinstein/changeo/src/017f7a65519b7c214d8aae786d7bee0069e2cd27/changeo/Gene.py#lines-387:401

Update docs.

[Jason Vander Heiden]

It's not the first D. It's whatever the D is in the row that has the first instance of the majority V call, majority J call, and the longest sequence length. (The D is just along for the ride with V/J/length consensus).