GitLab

Corrects bug introduced by 59a1bcf6.

096ab901 unleashes the power of 1a05fe6a and 422964cc.

core/fasta.{h,cpp}: default constructor also takes extract_field and extract_separator, factorize constructors

Even if we start from an empty Fasta, we should remember these values.

The constructor now uses the add() method which, itself, relies on the >> operator which has been overloaded.
Unit tests added for the add() method.

One could use constructor delegation for an even better factorisation but it
is C++11 only.

One may want to use several V (or D, or J) files for a unique germline, for example with TRDV + TRDD(D2).
(Now only the last file is really stored and indexed, but this will change soon.)

As KmerAffectAnalyser is only used with KmerAffect, we do not need to keep the templates.
The code should be easier to read for C++ newbies such as the author of this commit.

KmerStringAffect is no more used in the code.
If one day we would like to "store more things" in the affectations,
we could still extend KmerAffect with a pointer to something else.

Makes easier to compare two affect_infos structures (notably for unit tests)

Testing the function was not useless.

Accessing this method while the window is not label does not create an element in the map.

Previously we created small arrays of three integers to store information for backtracking.
Now we have a structure storing the same information so that we can allocate an array of structures.
Therefore we can allocate the whole array at once, and we don't need anymore to have plenty of allocations of three integers

Extracts the basename of a path. There is a basename() function in C but takes char *
(not even const char*), which is not convenient with string in C++.
And basename() doesn't remove extension.

Unit tests added.

This was hardcoded twice in the code.

This feature was not documented and not used.
The browser offers better normalization features.

This may help the upcoming modularization of vidjil.cpp

(Soissons)

Moreover, the argument 's' was not used

core/kmeraffect.{h,cpp}: remove 'kmer' argument to Kmer, KmerAffect and KmerStringAffect constructors

This argument was not used.
(Les Aubrais)

C++ polymorphism is awesome.
(Meung-sur-Loire)

AFFECT_AMBIGUOUS character is now '\1', in order to have a different value than AFFECT_UNKNOWN ('\0').

A IKmerStore maintains a list of labels that are used in the index.
This a step towards the removal of KmerStringAffect.

We can now create a Germline object without any index.

remove cluster with only one clone