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Bikeshed conf.js.sample, no tips by default

See merge request !508

doc/vidjil-format.md: corrections

See merge request !507

Thanks to the discussion with Patrice and @espyr.

Documentation on manually launching a backup

See merge request !506

See vdj#903

vidjil-format.md: Better document _average_read_length

See merge request !501

Feature tc/improve doc

See merge request !500

Following 7139afc6 the examples were not correctly modified, leading to some inconsistencies.

vidjil-format.md: minor update on seg fields

See merge request !499

Resolve "Implement null for normalized_reads"

Closes #3943

See merge request !485

If no read was segmented we may encounter an error in that case

Thonier Florian authored Jul 09, 2019 and Mikaël Salson committed Jul 15, 2019

Link to #3943

Thonier Florian authored Jul 09, 2019 and Mikaël Salson committed Jul 15, 2019

Link to #3943

IgReC replaces spaces with underscores

See merge request !496

Doing the opposite is not really satisfactory but, on the other hand, in such a case
we know the read name should contain spaces (because of the should-vdj format).

should-vdj-to-tap.py: --ignore_D option not working due to typo

Closes #3952

See merge request !494

Update repseq_vdj for mixcr

See merge request !495

doc/dev-{algo,client,server}.md: converted and split from dev.org

See merge request !491

Fixed and added some tests

Fix #3952

Feature t/3950 igrec parser

Closes #3950

See merge request !493

These *.py files should be moved to /tools

see #3950

Thanks to https://stackoverflow.com/a/8849771

should-vdj-to-tap.py: Wildcard must be at both places

See merge request !490

see #3932

pandoc --wrap=preserve --atx-headers -s -r org doc/dev.org -t gfm > doc/dev.md

Follows dbd61c55. Contrarily to the else case where the joker can
indifferently be placed before or after a term, it is not
the same when the term is a paranthesis expression.
Thus we need a joker both before and after to make sure we don't miss a case.

Alternative regex bug

Closes #3949

See merge request !489

We must allow anything *before* the alternative, not after (as in the else case)

Fix #3949

Link to #3943