Between get_updownstream_sequences and get_gene_sequence

Ensure that this sequence is properly analysed.

Update germlines

See merge request !247

Mikaël Salson authored Jun 26, 2018 and Mathieu Giraud committed Jul 12, 2018

Requires the environment variable COMPILERS to be defined

Test unit+should+valgrind: unit+should+shouldvdj took almost 3h.

Fix #3310 see vdj#450 for compiler installations on the slave.

Feature a/3004 : doc : convert in markdown and update

Closes #3348

See merge request !202

This is less readable but this avoids changing multiple tests
for the same reason (changing IGHV gene number)

See #3362

Thanks to #3364. See also #3349.

See #3364.

See #3364.

Thanks to @mikael-s.
See also #3349.

Therefore this sequence is not a bug anymore

Sequences are identical (on the region where the read is). Therefore we have
to offer alternatives.

It is not clear why the bugs are new.

Consequence of #3009

Changes in IMGT:
- Addition of 8 IGHV genes and alleles (8 F):IGHV1-8*03, IGHV1-69*15, IGHV1-69*16, IGHV2-26*02, IGHV2-26*03, IGHV2-70*15, IGHV2-70*16, IGHV2-70*17.
- Update of reference sequences of IGHV1-45*03 and IGHV2-70*04 (partial sequences were replaced with complete V-REGION).
- TRAJ13*02 reference sequence is AB258131.

See http://www.imgt.org/IMGTgenedbdoc/dataupdates.html

Other changes in MD5 should be due to changes in headers but this is not always true.
- IGKV2D-26*02 has gained 2 nucleotides at its end
- TRGV2*03 has appeared

We note that the new IGHV genes allow to diminish the number of ambiguous k-mers on S22 dataset

See #3348.

Closes #3348.

See #3348.

Fix aaf2e250.

Fix #3354

Closes #3354

See merge request !246

D7-27--J1 non-recombination should be warned

Closes #2232

See merge request !242

If the evalue is above the threshold we need to deactivate the optimization
to make sure that there is not a better solution.

Fix #3354

Allow it to assess the significance of an alignment.

algo/core/filter: typedef function<> doesn't seem portable

Closes #3361

See merge request !248

Was working on g++ 5 or 6 but not seven or 8.
Using using seems a good alternative.

Fix #3361

Feature a/3298 filter fine by default

Closes #3298, #3311, and #3210

See merge request !237

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

See also #3358/#3360.

This is the N length when there is no D.

See #2232.