Commit 780f3d7e authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: update online help, -2 can now be safely used

parent 83233122
......@@ -164,14 +164,17 @@ void usage(char *progname, bool advanced)
<< " -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
<< "Locus/recombinations" << endl
<< " -i try to detect incomplete/unusual recombinations (locus with '+', must be used with -g)" << endl
<< " -2 try to detect unexpected recombinations (must be used with -g)" << endl
<< endl ;
if (advanced)
cerr << "Experimental options (do not use)" << endl
<< " -I ignore k-mers common to different germline systems (experimental, must be used with -g, do not use)" << endl
<< " -1 use a unique index for all germline systems (experimental, must be used with -g, do not use)" << endl
<< " -2 try to detect unexpected recombinations (experimental, must be used with -g, do not use)" << endl
<< " -4 try to detect unexpected recombinations with translocations (experimental, must be used with -g, do not use)" << endl
<< " -! keep unsegmented reads as clones, taking for junction the complete sequence, to be used on very small datasets (for example -!AX 20)" << endl
<< endl
......
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