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See #3009

Feature a/3347 max clones

Closes #3347

See merge request !238

Feature a/3307 json fwd

Closes #3307

See merge request !229

Feature a/3293 seeds

Closes #3293

See merge request !226

Close #3307.

Use lib/json.hpp only when needed, and use lib/json_fwd.h elsewhere.
Yield a 40% speedup in build time on at least one platform.

See #3307.

See #3307 and next commit.

Closes #3347.
See also #3302.

See #3347.

Opens #3347.

Display the number of k-mer for each genes if debug_filter is defined

Closes #3346

See merge request !236

For more informations see #3346.

See #3259.

Reverts commit c0d14efb.
We don't need this extreme solution: coverage can be quick if not computing
branch coverage.

Coverage is now much quicker. The additional time for coverage over all the
jobs is about 3 min.

Fixes #3339

Perversely chosen mutations may fool our best heuristics.
See #3297 and #3298.

.gitlab-ci.yml: move coverage analysis to the end, set it manual

See merge request !233

See #3339. We want to have first fast tests.
Once we will have #3340, we will run again always this stage.

See #3293.

See #3293.

See #3293.

See #3293.

See #3293.

Opens #3293.

Feature a/3259 output filtered bioreader informations

Closes #3259

See merge request !231

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.

Since the original BioReader is called through every Filter's functions, it made
more sense to add it as an attribute in its class.

For more informations see #3259.

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

For more informations, see #3259.

For more informations see #3259.

Both of them are attributes stored in the Filter class.
filtered_sequences_calls is the number of times filterBioReaderWithACAutomaton is called
and filtered_sequences_calls is the number of sequences returned by this method.

For more informations see #3259.

Merge branch 'feature-a/3282-repetitive-filterbioreaderwithacautomaton-parts-to-reusable-function' into 'dev'

Feature a/3282 repetitive filterbioreaderwithacautomaton parts to reusable function

Closes #3282, #3312, and #3299

See merge request !228