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The CMD_SEGMENT scenario now tries the germlines in the multigermline (until the read is segmented).

On the default file, Vidjil now returns some clones even with default options.

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.

Methods are tested in specific conditions:
* at first position for countBefore
* at last position for countAfter
* when the affectation doesn't exist in the sequence

A hard-coded sequence should not be given to the constructor, instead it must be stored into a variable.

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

Testing the function was not useless.

Sequence is shorter than the seed

Compiler may optimise some lines which could change what gcov
sees as covered.

Even if the user is on the net, the server can be down...

Mathieu Giraud authored Oct 24, 2014 and Vidjil Team committed Oct 24, 2014

When storing the files in the db, web2py adds an hash.
There is no need to have a hash in the original filename (and it can produce files with too long filenames).

Mikaël Salson authored Oct 24, 2014 and Vidjil Team committed Oct 24, 2014

Putting the logs in the DB creates some deadlocks. Now we store them on disk.
We still need to add the info in DB so that we have all the info in DB.

Therefore output directory are not deleted anymore since they contain valuable information