Commit d50c2127 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: update help

parent 289965df
......@@ -157,8 +157,10 @@ void usage(char *progname, bool advanced)
<< " -D <file> D germline multi-fasta file (and resets -m and -w options), will segment into V(D)J components" << endl
<< " -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, IGK and IGL and sets window prediction parameters)" << endl
<< " -i multiple germlines, also incomplete rearrangements (must be used with -g)" << endl
<< " -g <path> multiple locus/germlines. In the path <path>, takes 'germlines.data' to select locus and parameters" << endl
<< " Selecting '-g germline' processes TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations" << endl
<< " A different 'germlines.data' file can also be provided with -g <file>" << endl
<< " -i multiple locus/germlines, also incomplete/unusual rearrangements (must be used with -g)" << endl
<< endl ;
if (advanced)
......
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