Commit f14cf7d5 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: update -h documentation, -uu

parent 8cbdbb88
......@@ -263,7 +263,7 @@ void usage(char *progname, bool advanced)
<< "Examples (see doc/algo.org)" << endl
<< " " << progname << " -c clones -G germline/IGH -3 data/Stanford_S22.fasta" << endl
<< " " << progname << " -c clones -g germline -i -2 -3 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 windows -g germline -i -2 -uu -U data/Stanford_S22.fasta # (detect the locus, splits all the reads into large files)" << endl
<< " " << progname << " -c segment -G germline/IGH -3 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
;
......
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