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See #3364.

Use same sequences for all germlines

Closes #3372 and #3373

See merge request !250

Partially revert 806f2180.
See #2645.

We also want to be able to take sequences from NCBI and gap them. See #2645.
Partially revert 806f2180.

file.py form() remove a query

See merge request !239

sample_set.py SampleSet.py fix sample_set sorting

Closes #3359

See merge request !244

This allows to use IMGT sequences even for up and downstream sequences.

The messages are saved and displayed at the end to ease the analysis of those warnings.

We need to ignore case as well as dots that can be introduced by
gapped sequences as well as comments that may be introduced by
missing Phe.

Otherwise it creates .1, .2, … files

See #3356.

Between get_updownstream_sequences and get_gene_sequence

Ensure that this sequence is properly analysed.

Feature a/3008 default j downstream

See merge request !148

Update doc

See merge request !249

* CI has changed for a while
* Compilation is now slightly different
* No more Debian package

Test for #3008

Doesn't seem to be new

Seems to go back in terms of J affectations. May be due to vdj#692.

See #3315. This is unrelated to #3008.

Sequences are short (or very short): offer several alternatives

Mathieu Giraud authored Jun 27, 2018 and Mikaël Salson committed Jul 12, 2018

See #3315.

TRGJ1*01 has one mutation while TRGJ2*01 hasn't. It's the only difference.
TRGJ1*02 is even slightly better as it has no mutation too but fewer deletions
at the 5' end.

This was detected because of #3148