Commit 2821fd02 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: updates help for -u option

This is really a debug option, because 'segmented.vdj.fa' is not a proper fasta file anymore.
parent e59972d4
......@@ -179,13 +179,15 @@ void usage(char *progname)
<< " -f <string> use custom Cost for fine segmenter : format \"match, subst, indels, homo, del_end\" (default "<<VDJ<<" )"<< endl
<< endl
<< "Debug" << endl
<< " -u output unsegmented sequences (default: " << UNSEGMENTED_FILENAME << ")" << endl
<< " and display detailed k-mer affectation both on segmented and on unsegmented sequences" << endl
<< "Output" << endl
<< " -o <dir> output directory (default: " << OUT_DIR << ")" << endl
<< " -p <string> prefix output filenames by the specified string" << endl
<< " -a output all sequences by cluster (" << SEQUENCES_FILENAME << ")" << endl
<< " -x no detailed analysis of each cluster" << endl
<< " -u output unsegmented sequences (default: " << UNSEGMENTED_FILENAME << ")" << endl
<< " -v verbose mode" << endl
<< endl
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment