Commit e65a9d36 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: warnings for non-optimal uses (-z, -A, -c segment)

parent e0a39a99
......@@ -118,6 +118,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define DEFAULT_SEGMENT_COST VDJ
// warn
#define WARN_MAX_CLONES 100
#define WARN_PERCENT_SEGMENTED 40
// display
......@@ -612,6 +613,33 @@ int main (int argc, char **argv)
cout << "# git: " << GIT_VERSION << endl ;
#endif
//////////////////////////////////
// Warning for non-optimal use
if (max_clones == -1 || max_clones > WARN_MAX_CLONES)
{
cout << endl
<< "* WARNING: vidjil was run with '-A' option or with a large '-z' option" << endl ;
}
if (command == CMD_SEGMENT)
{
cout << endl
<< "* WARNING: vidjil was run with '-c segment' option" << endl ;
}
if (max_clones == -1 || max_clones > WARN_MAX_CLONES || command == CMD_SEGMENT)
{
cout << "* Vidjil purpose is to extract very quickly windows overlapping the CDR3" << endl
<< "* and to gather reads into clones (-c clones), and not to provide an accurate V(D)J segmentation." << endl
<< "* The following segmentations are slow to compute and are provided only for convenience." << endl
<< "* They should be checked with other softwares such as IgBlast, iHHMune-align or IMGT/V-QUEST." << endl
<< "* More information is provided in the 'doc/algo.org' file." << endl
<< endl ;
}
//////////////////////////////://////////
// DISCOVER GERMLINES //
/////////////////////////////////////////
......@@ -1285,14 +1313,6 @@ int main (int argc, char **argv)
//reads = OnlineFasta(f_reads, 1, " ");
cout << "* WARNING: vidjil was run with '-c segment' option" << endl
<< "* Vidjil purpose is to extract very quickly windows overlapping the CDR3" << endl
<< "* and to gather reads into clones (-c clones), and not to provide an accurate V(D)J segmentation." << endl
<< "* The following segmentations are slow to compute and are provided only for convenience." << endl
<< "* They should be checked with other softwares such as IgBlast, iHHMune-align or IMGT/V-QUEST." << endl
;
Fasta rep_V(f_rep_V, 2, "|", cout);
Fasta rep_D(f_rep_D, 2, "|", cout);
Fasta rep_J(f_rep_J, 2, "|", cout);
......
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