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Mathieu Giraud authored Mar 05, 2019 and Mikaël Salson committed Mar 05, 2019

see #3764.

This was put in two different places and could lead to inconsistencies. Now the
reads are necessarily selected in the same way.

Mikaël Salson authored Nov 23, 2018 and Mathieu Giraud committed Nov 26, 2018

This avoids some issue with memory leak when leaving main earlier than expected.

See #3571

See #2828.

Following a discussion with @mikael-s.
We want to have meaningfull names when the sequence is not segmented.
See !320 (comment 126622)

See #3358.

We require in `vidjil-format.md` the unicity of the `id` fields.

See #3358.

See #3358.

See #3358.

See #3358.

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.

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 #3387.

Ad-hoc code for W61, D7-27/J1 non-recombined sequence.
Closes #2232.

See also #3358/#3360.

Closes #3347.
See also #3302.

Thanks to the work by @boreec, we now enable by default
the filtering for the second pass of the clone analysis.

When the computing time is dominated by the FineSegmenter
(such as with '-c clones -z 10000' or '-c segment'),
we get final speed-ups between 2x and 15x (#2360).

We could even set -Z 1 in most of the cases, but it should
be coupled with #3225. See also #3297 and #3344.

Close #3298.

See #3259.

See #3293.

See #3293.

See #3259.

Since we display the filter's informations in the main, it makes more sense
that this class has its own display method.

For more informations see #3259.

The Filter's informations are displayed for each germline at the end of execution.

For more informations, see #3259.

See #2732 and !212.

With g++-8 we had a “warning: catching polymorphic type * by value”.
This is solved by using a reference

Close #3294.

Use the macro UNUSED for mandatory parameters that are not
used within functions.

See #1233

Remove compiler warnings

See #1233

add_flag_function() is called only once.
Bug found thanks to CI.