Maj terminée. Pour consulter la release notes associée voici le lien :
https://about.gitlab.com/releases/2021/07/07/critical-security-release-gitlab-14-0-4-released/

Commit 598a2055 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: warning on '-c segment'

Vidjil should not be used to segment reads.
parent e8e73a5e
......@@ -133,7 +133,7 @@ void usage(char *progname)
cerr << "Command selection" << endl
<< " -c <command> \t" << COMMAND_WINDOWS << "\t window extracting (default)" << endl
<< " \t\t" << COMMAND_ANALYSIS << " \t clone analysis" << endl
<< " \t\t" << COMMAND_SEGMENT << " \t V(D)J segmentation" << endl
<< " \t\t" << COMMAND_SEGMENT << " \t V(D)J segmentation (not recommended)" << endl
<< endl
<< "Germline databases" << endl
......@@ -180,7 +180,7 @@ void usage(char *progname)
<< " -A reports all clones (-r 0 -R 1 -% 0 -z 0), to be used only on very small datasets" << endl
<< endl
<< "Fine segmentation options" << endl
<< "Fine segmentation options (second pass, see warning in doc/README)" << endl
<< " -d segment into V(D)J components instead of VJ " << endl
<< " -m <int> minimal admissible delta between segmentation points (default: " << DEFAULT_DELTA_MIN << ") (default when -d is used: " << DEFAULT_DELTA_MIN_D << ")" << endl
<< " -M <int> maximal admissible delta between segmentation points (default: " << DEFAULT_DELTA_MAX << ") (default when -d is used: " << DEFAULT_DELTA_MAX_D << ")" << endl
......@@ -203,7 +203,7 @@ void usage(char *progname)
<< "Examples (see doc/README)" << endl
<< " " << progname << " -G germline/IGH -d data/Stanford_S22.fasta" << endl
<< " " << progname << " -c clones -G germline/IGH -r 5 -R 5 -d data/Stanford_S22.fasta" << endl
<< " " << progname << " -c segment -G germline/IGH -d data/Stanford_S22.fasta" << endl
<< " " << progname << " -c segment -G germline/IGH -d data/Stanford_S22.fasta # (only for testing)" << endl
;
exit(1);
}
......@@ -1275,6 +1275,14 @@ int main (int argc, char **argv)
// déja déclaré ?
//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
<< "* or 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
;
while (reads->hasNext())
{
reads->next();
......
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