Commit ee762649 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: -h, add examples on LIL-L4

See #2635.
parent 866c3633
......@@ -263,8 +263,9 @@ void usage(char *progname, bool advanced)
<< " " << 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:IGH -3 demo/Stanford_S22.fasta # (restrict to complete recombinations on the IGH locus)" << endl
<< " " << progname << " -c windows -g germline/homo-sapiens.g -2 -uu -U demo/Stanford_S22.fasta # (detect the locus, splits all the reads into large files)" << endl
<< " " << progname << " -c segment -g germline/homo-sapiens.g -2 -3 -X 50 demo/Stanford_S22.fasta # (full analysis of each read, only for debug/testing, here on first 50 reads)" << 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
<< " " << progname << " -c segment -g germline/homo-sapiens.g -2 -3 -X 50 demo/Stanford_S22.fasta # (full analysis of each read, only for debug/testing, here on 50 sampled reads)" << endl
<< " " << progname << " -c germlines -g germline/homo-sapiens.g demo/Stanford_S22.fasta # (statistics on the k-mers)" << endl
;
exit(1);
......
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