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vidjil
vidjil
Commits
0c28aeb4
Commit
0c28aeb4
authored
Nov 05, 2014
by
Mathieu Giraud
Browse files
vidjil.cpp: update help, clarifying -d
parent
a969e65e
Changes
1
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algo/vidjil.cpp
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0c28aeb4
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@@ -145,7 +145,7 @@ void usage(char *progname)
<<
"Germline databases"
<<
endl
<<
" -V <file> V germline multi-fasta file"
<<
endl
<<
" -D <file> D germline multi-fasta file (
automatically
implies -d)"
<<
endl
<<
" -D <file> D germline multi-fasta file (implies -d)"
<<
endl
<<
" -J <file> J germline multi-fasta file"
<<
endl
<<
" -G <prefix> prefix for V (D) and J repertoires (shortcut for -V <prefix>V.fa -D <prefix>D.fa -J <prefix>J.fa) (basename gives germline code)"
<<
endl
<<
" -g <path> multiple germlines (experimental)"
<<
endl
...
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@@ -182,7 +182,7 @@ void usage(char *progname)
<<
endl
<<
"Fine segmentation options (second pass, see warning in doc/algo.org)"
<<
endl
<<
" -d segment into V(D)J components instead of VJ "
<<
endl
<<
" -d segment into V(D)J components instead of VJ
(and resets -m, -M and -w options)
"
<<
endl
<<
" -f <string> use custom Cost for fine segmenter : format
\"
match, subst, indels, homo, del_end
\"
(default "
<<
VDJ
<<
" )"
<<
endl
<<
endl
...
...
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