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I'm not sure what the case should be as some sequences are uppercase while others are lowercase.
Thus the regex should ignore case to be more robust.

If a genome position is available we get the upstream and downstream sequences
and paste it to the existing allele sequence.
Therefore now we always have to recover the allele sequence, which was not the
case before.

See #3009

See #3009

Used for #3009. We just want to get the upstream or the downstream
raw sequence to be able to paste it before the allele sequence by itself.
We need to take care on the sequence orientation.

fixup ncbi.py updown

Allow to reach up to 10 rq/sec instead of 3.
See here for having one : https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

We use this for reorganizing where tests are launched

See #3009.

Closes #3009 ? To be verified.

See #3009.

See #3009.

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.