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This reverts commit 53b44e2c.

In the second part of the test, the program verify that previous filtered
sequences are still in the BioReader when there is one more ex-aequo found.
For more informations about it, see #3279.

Cyprien Borée authored Jun 14, 2018 and Mikaël Salson committed Jun 15, 2018

In order to be sure that the filter function returns the accurates sequences,
every sequences is checked and also the size of them.

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

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.

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

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)

Cyprien Borée authored Jun 05, 2018 and Mikaël Salson committed Jun 13, 2018

For more informations see #3217

Cyprien Borée authored Jun 04, 2018 and Mikaël Salson committed Jun 13, 2018

This test assure that when a sequence is used to filter a BioReader, we
find the sequence back in the result when we provide '1' as the most significant
K-mer.
Also it assures that the final BioReader has a size less than the original one.

For more informations see #3217

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

(squashed from earlier commits)