Commit 4c2cf0fd authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp, doc/algo.org: multiple -g options and isotypes

parent 3938f68a
......@@ -156,7 +156,7 @@ void usage(char *progname, bool advanced)
<< " -# <string> separator for headers in the reads file (default: '" << DEFAULT_READ_HEADER_SEPARATOR << "')" << endl
<< endl ;
cerr << "Germline databases (one -V/(-D)/-J, or -G, or -g option must be given for all commands except -c " << COMMAND_GERMLINES << ")" << endl
cerr << "Germline databases (at least one -V/(-D)/-J, or -G, or -g option must be given for all commands except -c " << COMMAND_GERMLINES << ")" << endl
<< " -V <file> V germline multi-fasta file" << endl
<< " -D <file> D germline multi-fasta file (and resets -m and -w options), will segment into V(D)J components" << endl
<< " -J <file> J germline multi-fasta file" << endl
......
......@@ -201,7 +201,7 @@ clustering.
** Germline selection
#+BEGIN_EXAMPLE
Germline databases (one -V/(-D)/-J, or -G, or -g option must be given for all commands except -c germlines)
Germline databases (at least one -V/(-D)/-J, or -G, or -g option must be given for all commands except -c germlines)
-V <file> V germline multi-fasta file
-D <file> D germline multi-fasta file (and resets -m and -w options), will segment into V(D)J components
-J <file> J germline multi-fasta file
......@@ -223,8 +223,11 @@ Locus/recombinations
and using =-g germline/ -i -2= further test unexpected recombinations.
See [[http://git.vidjil.org/blob/master/doc/locus.org][locus.org]] for information on the analyzable locus.
- Analyzed locus and parameters are configured through the =germline/germlines.data= file.
A =germline/isotypes.data= file is provided to look for sequences with, on one side, IGHJ (or even IGHV) genes,
and, on the other side, an IGH constant chain.
To select a custom set of TR or Ig locus, you may copy =germline/germlines.data= into a new file,
as for example =germline/custom-germlines.data=, and run Vidjil with =-g germline/custom-germlines.data -i -2=.
- Several =-g= options can be used, as for instance =-g germline -g germline/isotypes.data=.
** Main algorithm parameters
......
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