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The D gene is trimmed but there are 7nt left. This should pass our
threshold. Should it?

We should have a C as N2 in the VDJ assignation.

Depending on the scoring scheme.

Fix f081f16f

May cause some issue when sequence is not segmented... we may find a CDR3.

It is hard to create a faulty test as it will depend on what was present in
memory before that.

Preliminary implementation, for vdj_assign

> pear.py > don't produce output file on failure
> don't reschedule run if pre-process has failed

We are not in maintenance anymore. By default, autodelete

Three nucleotides after one insertion and one mutation. This may be dubious.

At the moment the program can only be used to check one assignation.
It may be improved in the future.

display task scheduler result

before > true/false
after > WAIT/QUEUD/RUN/DONE/FAILED

adapt form o the selected pre_process

add separator

2 sequences with 3 or 4 exact nucleotides after the mutation

Whether you consider the mutation as being part of the V or not, you
have two possibilities.

Use the alternate syntax to take them into account

Deletion in 5'J is 5 instead of 6.

Checked against germline

48 VDJ sequences and 15 VJ/DJ/DDJ sequences, curated by Gary Wright