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This reverts commit 82c5ff15.

Those files are not used anymore and were there for tests purposes. This
commit should not have been merged.

This is not the optimal way.
See #3285.

optimize FineSegmenter, filtering BioReader with an Aho-Corasick automaton

Closes #920 and #3271

See merge request !199

Opens #3279.

Since kmer_threshold parameter became a signed int, there's the possibility
that this parameter is a negative number. If it's the case the entire original
BioReader is returned.

For more informations see #3268

Since a new parameter has been added to filterBioReader (representing the
filter specifity) it has to be transmitted when calling the function. Otherwise
the filter will do the filter on "NO_LIMIT_VALUE".

For more informations see #3268

Since a new parameter has been added, even the germline constructor call
in the test need to use it to use the automaton.

For more informations see #3268.

A boolean parameter has been added in the Germline constructors in order to
check if the automaton needs to be constructed or not.
For example with -Z all, the automaton is not constructed.

For more informations see #3268

The FineSegmenter constructor handles the filtering of the germline. By default
the value is "NO_LIMIT_VALUE", which means the filtering isn't active.

For more informations about it #3268.

In #3268 we want to add a specific command-line option for the filtering.
The -Z has only been declared in the getopt. The remaining task is to
check if -Z still has NO_LIMIT_VALUE as an argument. If so the automaton
is not built, otherwise the automaton is built and the argument is used to
filter the BioReader.

If the program is call with -Z 0, the filter function use every K-mer with
at least one match. 0 is defined by the constand ALL_KMERS_VALUE in tools.h
For more informations see #3276

This constant is representing -Z 0 parameter. It's used when the filter function
is called on every k-mer with at least one match.

For more informations see #3276

Since in the future there might be another automaton (automaton_3), the
pair_automaton variable has been changed to automaton_5 in many files.

see #3267 and #3267 (comment 96152)

Since the kmer_threshold parameter became a signed integer, some comparison
were producing sign warnings due to -Wsign-compare g++ compiler.

For more informations see #3270

Since the threshold parameter can be -1 the threshold parameter has been switched
to a signed integer (the default int in C/C++).
Also the use of NO_LIMIT_VALUE is used insted of -1.

For more informations see #3270

Since the new option -Z will be added, the case where all K-mers will be selected
to filter will be represented by -Z -1.
For more informations about it, see #3268 and #3264.

For the purpose of adding the -Z option (described in #3264), the -H option
will show its description.

Incidentally close #3271.

Sequences are equal before 110bp so the alternative is valid.

For more informations see #3262

Since some sequences are identical, we can add them as a result for
the test.

For more informations about it, see #3223 and #3262.

Since some sequences are identical, we can add them as a result for
the test.

For more informations about it, see #3223 and #3262.

When there is no sequences found in the filtered BioReader it throws a
segfault.

For more informations about it, see #3223

For more informations see #3217

To get the genes with the same number of occurences (described in #3217 )