Commit 92fc05f5 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: help, update examples

parent ba93cde1
......@@ -253,11 +253,11 @@ void usage(char *progname, bool advanced)
<< 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
<< " " << progname << " -c clones -G germline/IGH data/Stanford_S22.fasta" << endl
<< " " << progname << " -c clones -g germline -i -2 data/Stanford_S22.fasta # (detect the locus for each read, including unusual/unexpected recombinations)" << endl
<< " " << progname << " -c windows -g germline -i -2 -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 # (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);
}
......
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