There is a problem in g++4.8: erase with a const_iterator doesn't exist
(while it should: it is c++11).

See also #3502.

See also #3502.

With #3225 we don't have a fixed limit on the number of sequences to get.
We will get all the sequences that have a common number of k-mers close to the first sequence.

A higher p-value threshold will give a lower limit for number of k-mers hence will be more sensitive (but less time-efficient).
See #3225

This will ease unit testing

Rather we use an uncertainty range (see #3225 for why and how).

It is necessary to get the length of the longest transferred sequence as it
will be used as a reference to compute the empirical probablity that a k-mer
has matched in the longest possible sequence. Therefore we make the assumption
that k-mers matched in the longest sequence but we have no way of knowing as
we don't keep track of where the k-mers matched.

Fixes #3225

Compute the minimal number of k-mers of an uncertainty range whose mean is
given by the empirical number of k-mers found.

The probability is provided as an integer as we don't have Z-scores for every
possible value and float comparison can be a bit tricky.

See #3444.

Factor a code that what called 4 times.

Fixes #3395

See #3393

See #3393

Will be called when not all the reads can be stored.

See #3393

This will help to reuse those functions elsewhere in the code

See #3393

Don't know why and since when (see should#20)

See #3414.

From #2549

What was tested was not output anymore by fuse.py.
This replaces the test with something somewhat similar that is now output.
That also ensure the distribution is slightly tested.

The sequence is now correctly found as TRG.

From #2549

The sequence is now correctly found as TRG.

See #1409.

For more informations, see #1409.

Now the option can be used with a number in order to export the alternative
genes into the json.

For more informations, see #1409.

For more informations, see #1409.

This pointer is necessary to have the Bioreader where the N best genes will be
exported.

For more informations, see #1409.