Commit 6fa07171 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: experimental '-1' option, builds all germlines into the same index

It is currently not working.
parent 16602f94
......@@ -156,7 +156,11 @@ void usage(char *progname)
<< " -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 (in the path <path>, takes TRA, TRB, TRG, TRD, IGH, IGK and IGL and sets window prediction parameters)" << endl
<< " -i multiple germlines, also incomplete rearrangements (must be used with -g)" << endl
<< endl
<< "Experimental options (do not use)" << endl
<< " -I ignore k-mers common to different germline systems (experimental, must be used with -g, do not use)" << endl
<< " -1 use a unique index for all germline systems (experimental, must be used with -g, do not use)" << endl
<< endl
<< "Window prediction" << endl
......@@ -318,7 +322,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "AX:haiIg:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uUK3")) != EOF)
while ((c = getopt(argc, argv, "AX:haiI1g:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uUK3")) != EOF)
switch (c)
......@@ -373,6 +377,10 @@ int main (int argc, char **argv)
case 'I':
multi_germline_mark = true;
case '1':
multi_germline_one_index_per_germline = false ;
case 'G':
germline_system = string(optarg);
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