See #3785.

See #3785.

Bye-bye -FaW, see #3785.

See #3782 and #3295.

See #3295.

See #3295.

Use the new option names.
Remove also '--trim 0' options used in some tests.

See #3295.

Following passionate discussions (!245) :
 - add many long option names, using updated terms
 - deprecate 11 short options, including many rare options coming form ancient times
 - reorder options and bikeshed some help texts

See #3295.

Ensure tab after name

See merge request !430

On each line we should have a + or - when segmented or an exclamation mark
when unsegmented.
A tab should always exist at least between the sequence name and the VDJ designation.

This should ease parsing the output.

-c designations

Closes #3772

See merge request !429

Better CLI11 error messages, link to documentation

See merge request !428

see also should#31

Add display the error message improved in the previous commit.

see #3775

close #3772.

define and use failure_message_doc(), taking inspiration from FailureMessage::simple()

see #3775

See #3772.

See #3772.

Feature cs/3722 browsers from env or file

See merge request !423

This cannot be properly tested in test_segmenter_page_errors.rb as we don't have a menu there

See #3722 and #3701.

tests/launch_functional_tests: select browsers from environment variable or from 'tested-browser' file

Partially revert 02ca0a24.
We want both to agnostically use 'launch_functional_tests', but also to be able to follow in a versioned file
the supported browsers.

Use a fixed version of web2py

Closes #3605

See merge request !419

Update e-value on SEG_METHOD_ONE with Aho

Closes #3773

See merge request !426

was done twice in 40aef950 and 556d8b0b, but git merge
did not understood what we meant there ;-)

see #3773

Random read sample for representative

Closes #3764

See merge request !422