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editing permissions or deleting a patient was broken due to the wrong id
being passed to the controller.

just a little more info on the init_db form.

in the same vein as setting the admin password for users, the web2py
admin password is not easy to change once web2py itself has been
installed. Therefore defaulting it to the same as the vidjil admin
passwords seems like a good option

We're moving towards distributing vidjil so it's important to allow
users to choose their admin email and password.

This is due to the Aho-Corasick automaton where we now have an index load for
the V gene and for the J gene. There is only one matching kmer from IGLJ but
that's enough to have an evalue < 1 because the index load for IGLJ is very
low and because there are only two reads in the dataset.

We could put a -e 1e-1 on the command line to make the test pass. Would this
be hacky or not?

This test passed because the 2 matched the 241 of the read length. But this is
not what we wanted to test. We expect just one sequence to be ambiguous.

This is necessary (for instance) with xxx germlines.

Kmer indexes and Aho-Corasick don't have the same features.
While it is possible to deal with several seeds in Aho-Corasick it is not with a simple lookup table.
Therefore we can consider different seeds only in some cases.

Launching init several times will allocate several times score_bins and nb_scores
which will cause memory leaks.

This is particularly the case in the WindowExtractor() which calls BinReadStorage
on germline->code but we can have different germlines with the same germline->code.

The default index will be set to Aho-Corasick when we'll
consider that it is ready. For now, option -q (quick) can launch AC automaton

Makes it ready to support a parameter to choose the index.

Allows to build any type of index instead of relying on one specific type.

This has been moved in another file for better code separation.

It will be useful to determine the type of index to build at runtime.

The affectation length is longer with Aho-Corasick than with k-mer based
indexes. So we use the length of the read instead.

The length of the affectations must be the seed span and not the seed weight
as the dashes are replaced by actual letters.

Unit test added.

This makes possible to compare affectations regardless of their length.

Some indexes store global informations regarding all the kmers (ArrayKmerStore and MapKmerStore).
Other indexes have a more detailed view on the kmers that are stored (Aho-Corasick automaton).
These indexes are more accurate on the index load per affectation.

Go back to the previous computation. Don't use kmer.getLength() to compute
the index load since it is not properly set with the UNKNOWN or NOT_UNKNOWN
affectations.

Depending on the length of the affectation, we may not have the same results

At first, we considered that smallestAnalysableLength() would be enough
to deal with differences between a k-mer index and an Aho-Corasick automaton.
This is actually not the case.

We need to have the length of the seed together with the affectation for the
Aho-Corasick automaton. In the end this allows to get the same affectation
strings than with a k-mer index. This would not have been possibble with the
smallesAnalysableLength() function and it makes it useless.

This will be useful for Aho-Corasick automaton to put
the affectation at the right place.

To determine whether two affectations are equal, we don't need to check
their length for the unknown and ambiguous affectations. They could
even differ. The length of an ambiguous affectation would be the length
of the affectations causing the ambiguity

Needed with the Aho-Corasick automaton (because of using a map)

The germline may have an index but also sub-germlines (eg. for XXX
germline). All of them must be finished.

When the germline by itself didn't insert any kmer but relies
on other germlines (eg. for the XXX germline), we compute the
index load by relying on the index load of the other germlines.

Note that the sum may not accurately reflect the index load
(as there may have common k-mers between the germlines).

It prevents from finishing several times (which may cause some troubles)