merge - JUNCTION/CDR3 detection based on Cys104 and Phe118/Trp118 position
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.
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