Commit a1c70cd9 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: -h, our first example in on Demo-X5 rather than on S22

See #2635.
parent eb27a50f
......@@ -260,8 +260,9 @@ void usage(char *progname, bool advanced)
<< endl
<< "Examples (see doc/algo.org)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g -2 -3 demo/Stanford_S22.fasta # (basic usage, detect the locus for each read," << endl
<< " # including unexpected recombinations, analyzes CDR3)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g -2 -3 -r 1 demo/Demo-X5.fa # (basic usage, detect the locus for each read," << endl
<< " # cluster reads and report clones starting from the first read (-r 1)," << endl
<< " # including unexpected recombinations (-2), assign V(D)J genes and try to detect the CDR3s (-3))" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g:IGH -3 demo/Stanford_S22.fasta # (restrict to complete recombinations on the IGH locus)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g -2 -3 -z 20 demo/LIL-L4.fastq.gz # (basic usage, output detailed V(D)J analysis on the first 20 clones)" << endl
<< " " << progname << " -c windows -g germline/homo-sapiens.g -y 0 -uu -U demo/LIL-L4.fastq.gz # (splits all the reads into (large) files depending on the detection of V(D)J recombinations)" << endl
......
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