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Follows edd001ee: the downstream sequence was the one from IGHJ1 instead of IGLJ1.

see #3518

link to #3518

The sequence is now correctly found as TRG.

The sequence is now correctly found as TRG.

Test for #3008

Doesn't seem to be new

See #3315. This is unrelated to #3008.

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

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

The start of TRGJ2*01 is identical (seen as a consequence of #3148)

We find a TRGJ2*01 gene with 3 deletions at the start and an exact alignment
while the TRGJ1*02 has 0 deletion and no differences. However for us the
alignment with TRGJ2*01 is longer because we were unable to correctly retrieve
the downstream sequence for the allele TRGJ1*02 (see #3009).

See #3008.

See !148 (comment 83304)
for more information on this change.

IGKJ4*02 has more mutations but aligns on the whole length of the sequence.

At the time this test was made, we didn't launch Vidjil for looking unexpected recombinations.
This is the case for quite some time now and this sequence should have been found as unexpected
but a bug (see #3296) prevented it to be found.

This is now corrected.

With the previous format the BUG keyword was ignored.
We also specify that the bug occurs at the locus level.

See #3296 for the bug.

This is unrelated to this issue.

See #3145 and #3146.

The junction is given neither by IgBlast nor by IMGT (the latter correctly
finds the V/J genes though).

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

The expected V part can be found in multiple known V, thus alternative were added.

For more informations see #3298.

Sequences are equal before 110bp so the alternative is valid.

For more informations see #3262

Since some sequences are identical, we can add them as a result for
the test.

For more informations about it, see #3223 and #3262.

Since some sequences are identical, we can add them as a result for
the test.

For more informations about it, see #3223 and #3262.

The tests have been moved in a should-get test

Not working for the momeent. 
need to use specific ikaros germline file.

See #2635.

IGHJ4*02 is actually slightly better than IGHJ4*01, because one insertion and
one deletion (with IGHJ4*01) are replaced with two substitutions (IGHJ4*02)

This deletion length is too large and we have problems with the e-value which is too high.
See #2767 #2124

IGH4-59*03 is a good choice, IGHV4-59*04 is not.