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As raised by @magiraud in !182 the parameters are far from being obvious

Feature g/3148 germline order

Closes #3148

See merge request !243

Having a key for upstream and downstream data is not adapted to our current needs.
Different sequences may share a common accession number which then leads to a problem
when outputting sequences (see #3148).

Followed @magiraud suggestion: #3148 (comment 104665)

Make sure that IGHD and IGHD+up orders are identical and that the
IGHD+up looks ok.

See #3148

Half-time merge, closes #3009.
See !182.

Not sure that the l flag from should.py could nicely apply here.

In the XML output the coordinates are 0-based: “returns the chromosomal
position of that gene in 0-based coordinates”
https://www.ncbi.nlm.nih.gov/books/NBK179288/

Are you serious guys?

chromosome:GRCh38:14:105916826:105916885:-1

See #3009

We are aware that the header is not correct. However this is not new.

See !182

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