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  -c COMMAND                  command
        clones       locus detection, window extraction, clone clustering (default command, most efficient, all outputs)
        windows      locus detection, window extraction
        segment      detailed V(D)J designation (not recommended)
        germlines    statistics on k-mers in different germlines

Remplace-t-on segment par ce qui suit ?

        designate      detailed V(D)J designation, without prior clustering (not as efficient)

Et l'avertissement :

* WARNING: vidjil-algo was run with '-c segment' option
* vidjil-algo efficientl extracts windows overlapping the CDR3
* to cluster reads into clones ('-c clones').
* Computing accurate V(D)J designations for many sequences ('-c segment' or large '-z' values)
* is slow and should be done only on small datasets or for testing purposes.
* More information is provided in the 'doc/vidjil-algo.md' file.

Avant-dernière ligne, à la place :

* is not as efficient as the default '-c clones' command

Et on enlève "should be done only on small datasets or for testing purposes" ?

Voir aussi #3295 (closed).