Commit 29f49c02 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: update warnings for '-c segment' and large '-z' options

parent 379d0983
......@@ -803,7 +803,7 @@ int main (int argc, char **argv)
//////////////////////////////////
// Warning for non-optimal use
if (max_clones == -1 || max_clones > WARN_MAX_CLONES)
if (max_clones == NO_LIMIT_VALUE || max_clones > WARN_MAX_CLONES)
{
cout << endl
<< "* WARNING: vidjil was run with '-A' option or with a large '-z' option" << endl ;
......@@ -815,11 +815,12 @@ int main (int argc, char **argv)
<< "* WARNING: vidjil was run with '-c segment' option" << endl ;
}
if (max_clones == -1 || max_clones > WARN_MAX_CLONES || command == CMD_SEGMENT)
if (max_clones == NO_LIMIT_VALUE || 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 full V(D)J designations are slow to compute and are provided only for convenience." << endl
cout << "* Vidjil's purpose is to efficiently extract windows overlapping the CDR3" << endl
<< "* to gather reads into clones ('-c clones')." << endl
<< "* Computing accurate V(D)J designations for many sequences ('-c segment' or large '-z' values)" << endl
<< "* is slow and should be done only on small datasets or for testing purposes." << endl
<< "* More information is provided in the 'doc/algo.org' file." << endl
<< endl ;
}
......
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