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I finally understood how to use CLI11 callbacks.
See https://cliutils.gitlab.io/CLI11Tutorial/chapters/advanced-topics.html

Close #2749.

See #3292.

Closes #2741.

Replays 86e788fc.

Some options will be not always displayed in the help message.
Replays da89488c.

Replays d971892b.
See #2739.

Don't show invisible clones

Closes #3291

See merge request !211

Fixes #3291 and follows f8075d81

We make a clone supported by 0 read so that it
should not be visible. We choose a clone whose
top < 50 so that it should be visible if its size
was > 0.

get-saved-germline: Prevent error message when folder doesn't exist

See merge request !205

Releasing algo via Gitlab CI

Closes #3002

See merge request !206

Correct segault on filtering

Closes #3284

See merge request !207

Resolve "boucle recursive infinie avec la fonction compare"

Closes #3288

See merge request !208

See #3288

The second part of the test now verify that previous sequences are still
in the filtered BioReader even though a new ex-aequo has been found.

For more informations see #3284

This reverts commit 53b44e2c.

Use easiest comparaisons bettween two values.
fix #3288

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.

Put braces for better lisibility

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

For more informations see issue #3279

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

Since the last way to compare produced segfault (due to undefined behaviour
of the advance method), to bypass this problem we just look at the previous
of occurences to see if it's the same as the last -1.
For more informations 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.

See #3002

See #3002

This ensures that the following stages won't be run.
See https://gitlab.com/gitlab-org/gitlab-ce/issues/25892

See #3002

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