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Implements affine gaps by storing three matrices, B, Bins and Bdel.

Re-organization, equivalent code

Not everything is tested yet in WindowsStorage.
In particular getSample, getLabel, setIdToAll are not tested

If you would know the two most frequent affectations in a read, what could you do ?

Not using a pointer creates some problems with KmerSegmenter.
We should have a copy constructor in KmerSegmenter but it is a pain in the ***.

Not using pointers makes several copies of the same object. However the copies share the
same pointer to a KmerAffectAnalyser and that's the problem. When one of the copy is
deleted, its destructor is called which will delete the KmerAffectAnalyser and the other
copies won't have access to it, and it will also generate an error when the copies will try
to delete the KmerAffectAnalyser.

This has been solved by using pointers to KmerSegmenter everywhere.

This was dead code.

This was dead code, not working, with less features than ./vidjil -u

This was dead code, not working, with less features than tools/align.cpp

As the 'operation' struct now contains the score, the S table is useless.

An homopolymer is now aligned as CC/-C instead of CC/C-.
Side effect from previous commit.

Edit operations, with their score computation and their backtracking information,
are now defined in a unique location.
The code should thus be more flexible and easier to read and maintain.

When using different indexes, this is only a cosmetic change.
But it prepares ourselves to use an unique index, possibly with a better indexing structure.

This was not a .fa file, and now it contains all reads.

Now 'out_unsegmented' causes are output in segment.cpp, displaying affectation for each germline

Unit tests are passing again.
The code is now clearer, as these tests actually tested segmentation on only one germline.
We should now have real unit tests on KmerMultiSegmenter.

Same tests than multi-{complete,short}.should_get, but this time with -i.
Testing for incomplete rearrangements should not prevent the 7 reads
from being recognized in the right (complete) system.

multi-complete.fa -> 7 reads (1 per system), exact concatenation V+(D)+J, no deletion, no insertion
multi-short.fa -> the same 7 reads, but shortened (especially at V end)

This should be corrected.

This is an important change in how the heuristics works with multi-germlines.

Now the segmentation may run 2x to 3x slower (with -g -i), but we ensure that
the best germline is selected for each read. This improves the results,
in particular with mixed data from regular and incomplete rearrangements.

All the germline stats are now updated in core/windowExtractor.cpp.

This option is sponsored by UPMC.

Such as TRD/TRD+