Commit 673e918c authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: update usage message, commands

parent fc50297b
......@@ -142,10 +142,11 @@ void usage(char *progname)
cerr << "Usage: " << progname << " [options] <reads.fa/.fq/.gz>" << endl << endl;
cerr << "Command selection" << endl
<< " -c <command> \t" << COMMAND_WINDOWS << " \t window extracting" << endl
<< " \t\t" << COMMAND_CLONES << " \t clone gathering (default)" << endl
<< " \t\t" << COMMAND_SEGMENT << " \t V(D)J segmentation (not recommended)" << endl
<< " \t\t" << COMMAND_GERMLINES << " \t discover all germlines" << endl
<< " -c <command>"
<< "\t" << COMMAND_CLONES << " \t locus detection, window extraction, clone gathering (default command, most efficient, all outputs)" << endl
<< " \t\t" << COMMAND_WINDOWS << " \t locus detection, window extraction" << endl
<< " \t\t" << COMMAND_SEGMENT << " \t detailed V(D)J segmentation (not recommended)" << endl
<< " \t\t" << COMMAND_GERMLINES << " \t statistics on k-mers in different germlines" << endl
<< endl
<< "Germline databases (one -V/(-D)/-J, or -G, or -g option must be given for all commands except -c " << COMMAND_GERMLINES << ")" << endl
......@@ -223,6 +224,8 @@ void usage(char *progname)
<< endl
<< "Examples (see doc/algo.org)" << endl
<< " " << progname << " -c clones -G germline/IGH -r 5 data/Stanford_S22.fasta" << endl
<< " " << progname << " -c clones -g germline -r 5 data/Stanford_S22.fasta # (detect the locus for each read)" << endl
<< " " << progname << " -c windows -g germline -u -U data/Stanford_S22.fasta # (detect the locus, splits the reads into two (large) files)" << endl
<< " " << progname << " -c segment -G germline/IGH data/Stanford_S22.fasta # (only for testing)" << endl
<< " " << progname << " -c germlines data/Stanford_S22.fasta" << endl
;
......
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