This is perhaps not the best solution, as should-to-tap.sh becomes specific to these tests.

This will be more flexible.

The germline files now contain gapped V and J sequences.
This may have one day a side effect on browser/js/germline.js.

The JUNCTION/CDR3 detection (-3) works more reliably.
As in IMGT/JunctionAnalysis, the detection relies on the positions of Cys104 and Phe118/Trp118.
The detection is here in O(n), taking advantage of the already aligned V and J segments.
We use V gapped sequences from IMGT, and J gapped sequences that we compute,
based on the Phe/Trp-Gly-X-Gly pattern.

This was realized after prototyping and tests by @flothoni.

Clean stdout. We just report here the JUNCTION, including Cys104 and Phe118/Trp118.

Many people are used to have the full JUNCTION, including Cys104 and Phe118/Trp118.
We thus output both 'cdr3' and 'junction' fields in the json output.

We compute CDR3startJfull directly from JUNCTIONend.

This solves the problem identified in 0aae0cf8.

Will be used to test CDR3/JUNCTION detection.