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.

All full codons aligned with the J germline gene are translated according to this frame.

This was realized after prototyping and tests by @flothoni.
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.

The current implementation will not give a precise positions when there are insertions or deletions
between Cys104 and the end of the V segment  (or between the start of J segment and Phe118/Trp118).
This could be improved by backtracking the DP matrix.

This further cleans the code and allows to output D1/D2 boxes as well.

One day, we may change '5del' and '3del' fields, their naming is not so consistent.

This was not used and not symmetrical.

Bug detected thanks to a full Valgrind.

Discussion with @mikael-s and @flothoni.

We now run another dynamic programming once the overlap was handled -- only
on the best reference sequence -- to check the actual e-value of the D segment.

Vidjil Team authored Feb 03, 2016 and Mathieu Giraud committed Feb 05, 2016

We do not want to detect twice the same D gene.
Note that we do not currently forbid alleles of a same gene.

Discussion between @flothoni, @mikael-s, and @magiraud.

Vidjil Team authored Feb 03, 2016 and Mathieu Giraud committed Feb 05, 2016

When a D has already been detected, we do not want to detect anything inside this D.
Before this commit, spurious D detections could happen in the EXTEND_D_ZONE.

Discussion between @flothoni, @mikael-s, and @magiraud.

When a D segment has been detected, we now try to detect an additional D between V/D or between D/J,
possibly detecting VDDJ (or even some VDDDJ) recombinations.

Note that this detection is not optimal. A chaining algorithm would be preferable here.
Moreover, statistics should be refined, as now the only filter is done before check_and_remove_overlap.

We need to store sequence_or_rc in the Segmenter.

Previously, we have at many places things like "int *del_DD_left, int *DD_start, int *best_DD, int *DD_end, int *del_DD_right".
This was not so clean and error-prone. Now all these parameters are stored into a ‘AlignBox’ object.
This will lead to further simplifications of the code, better code maintenance, and allow some extensions.

We would like to call that on other places than between the V and the J.

We factorize some computations (seq_left, seq_right, seg_N).
This is the last commit of the day sponsored by the CERNA.

This enables in particular the analysis of +Vk/-Vk recombinations.
This commit is again sponsored by the CERNA.

Until now, the FineSegmenter tested both strands, resulting in a code duplication and in
unnecessary computations.

This improvement is sponsored by the CERNA.