Commit 06ada6e9 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: update command-line help

New features with -g.
-g is the recommended way, -V/-D/-J/-G are more advanced.
parent f7339baf
......@@ -158,14 +158,16 @@ void usage(char *progname, bool advanced)
<< " -# <string> separator for headers in the reads file (default: '" << DEFAULT_READ_HEADER_SEPARATOR << "')" << endl
<< endl ;
cerr << "Germline databases (at least one -V/(-D)/-J, or -G, or -g option must be given for all commands except -c " << COMMAND_GERMLINES << ")" << endl
<< " -V <file> V germline multi-fasta file" << endl
<< " -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 locus/germlines. In the path <path>, takes '" << DEFAULT_MULTI_GERMLINE_FILE << "' to select locus and parameters" << endl
<< " Selecting '-g germline' processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations" << endl
<< " Files different than '" << DEFAULT_MULTI_GERMLINE_FILE << "', for example for other species, can also be provided with -g <file>" << endl
cerr << "Germline databases (at least one -g or -V/(-D)/-J option must be given for all commands except -c " << COMMAND_GERMLINES << ")" << endl
<< " -g <.g file>(:filter)" << endl
<< " multiple locus/germlines, with tuned parameters." << endl
<< " Common values are '-g germline/homo-sapiens.g' '-g germline/mus-musculus.g'" << endl
<< " The list of locus/recombinations can be restricted, such as in '-g germline/homo-sapiens.g:IGH,IGK,IGL'" << endl
<< " -g <path> multiple locus/germlines, shortcut for '-g <path>/" << DEFAULT_MULTI_GERMLINE_FILE << "'" << endl
<< " processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations" << endl
<< " -V <file> custom V germline multi-fasta file" << endl
<< " -D <file> custom D germline multi-fasta file (and resets -m and -w options), will segment into V(D)J components" << endl
<< " -J <file> custom J germline multi-fasta file" << endl
<< endl
<< "Locus/recombinations" << endl
......@@ -261,11 +263,12 @@ void usage(char *progname, bool advanced)
<< endl
<< "Examples (see doc/algo.org)" << endl
<< " " << progname << " -c clones -G germline/IGH -3 data/Stanford_S22.fasta" << endl
<< " " << progname << " -c clones -g germline -i -2 -3 data/Stanford_S22.fasta # (detect the locus for each read, including unusual/unexpected recombinations)" << endl
<< " " << progname << " -c windows -g germline -i -2 -uu -U data/Stanford_S22.fasta # (detect the locus, splits all the reads into large files)" << endl
<< " " << progname << " -c segment -G germline/IGH -3 data/Stanford_S22.fasta # (full analysis of each read, only for debug/testing)" << endl
<< " " << progname << " -c germlines data/Stanford_S22.fasta # (statistics on the k-mers)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g -2 -3 data/Stanford_S22.fasta # (basic usage, detect the locus for each read, including unusual/unexpected recombinations)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g:IGH -3 data/Stanford_S22.fasta # (restrict to IGH complete locus)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g -2 -3 data/Stanford_S22.fasta # (detect the locus for each read, including unusual/unexpected recombinations)" << endl
<< " " << progname << " -c windows -g germline/homo-sapiens.g -2 -uu -U data/Stanford_S22.fasta # (detect the locus, splits all the reads into large files)" << endl
<< " " << progname << " -c segment -g germline/homo-sapiens.g -2 -3 data/Stanford_S22.fasta # (full analysis of each read, only for debug/testing)" << endl
<< " " << progname << " -c germlines data/Stanford_S22.fasta # (statistics on the k-mers)" << endl
;
exit(1);
}
......@@ -659,7 +662,7 @@ int main (int argc, char **argv)
if (!germline_system.size() && (command != CMD_GERMLINES))
{
cerr << ERROR_STRING << "At least one germline must be given with -V/(-D)/-J, or -G, or -g." << endl ;
cerr << ERROR_STRING << "At least one germline must be given with -g or -V/(-D)/-J." << endl ;
exit(1);
}
......
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