Commit bae1a8a6 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: command-line help, update, remove duplicate

Completes 06ada6e9.
parent a8f58f8b
......@@ -262,9 +262,9 @@ void usage(char *progname, bool advanced)
<< endl
<< "Examples (see doc/algo.org)" << 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 clones -g germline/homo-sapiens.g -2 -3 data/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 data/Stanford_S22.fasta # (restrict to complete recombinations on the IGH locus)" << 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 -g germline/homo-sapiens.g data/Stanford_S22.fasta # (statistics on the k-mers)" << endl
......
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