Commit c9769b2c authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: option '-i' can now be safely used

With the updated multi-germline heurisitic (ad552cb7), selecting -i is safer now.
See in particular tests/multi-i(-short).should_get (2ade70be).
parent 6424aa09
......@@ -153,7 +153,7 @@ void usage(char *progname)
<< " -J <file> J germline multi-fasta file" << endl
<< " -G <prefix> prefix for V (D) and J repertoires (shortcut for -V <prefix>V.fa -D <prefix>D.fa -J <prefix>J.fa) (basename gives germline code)" << endl
<< " -g <path> multiple germlines (in the path <path>, takes TRA, TRB, TRG, TRD, IGH and IGL and sets window prediction parameters)" << endl
<< " -i multiple germlines, also incomplete rearrangements (experimental, must be used with -g)" << endl
<< " -i multiple germlines, also incomplete rearrangements (must be used with -g)" << endl
<< " -I ignore k-mers common to different germline systems (experimental, must be used with -g, do not use)" << endl
<< endl
......
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