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(n * n) may be too large for an int when (n) is large.

The problem detected in 0eccf628 is now corrected.

Fixes a bug introduced in 90b8bb4e

The germline package has now a correct germline.js.

There are minor differences in the IMGT header of some sequences.
There is still something happening on IGHD_upstream.

A collection of sequences on all locus, gathered from other files.

This somewhat restores a test removed in 0ae4e1e6.

tests/should-vdj-to-tap.py: option '-D', ignore gene/allele names for D genes in .should-vdj patterns

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.

This is the only test checking the raw json output.

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.

These mixed TRA/TRD VDDJ sequences should be further studied.

Back in april 2013, when @mikael-s designed this simulated sequence,
he premonitorily included a borderline case of a VDDJ recombination.
There are here 6-7 nucleotides exactly conserved for the second D.

The second D has 20 nucleotides that are exactly conserved.

We are confident enough to use '-d' on our should-vdj tests.

VDDJ segmentation is still somewhat experimental.
Moreover, it will have someday some consequence on the json output, that are not always desirable.
We prefer thus to keep this optional.

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.

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.