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vidjil.cpp, core/germline.cpp: refactor, streamlining germline declaration

Mathieu Giraudrequested to merge
feature-a/4845-refactor-vidjil-germline into dev

Handle with the same way -V/-D/-J and -g options.

See #4845 (closed). Incidentally close #4844 (closed).

Edited by Mathieu Giraud

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