Commit e4fa6c7a authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: online help, fix deprecated options

parent e407e7ab
......@@ -427,7 +427,7 @@ int main (int argc, char **argv)
bool keep_unsegmented_as_clone = false;
app.add_flag("--not-analyzed-as-clones", keep_unsegmented_as_clone,
"consider not analyzed reads as clones, taking for junction the complete sequence, to be used on very small datasets (for example --not-analyzed-as-clones -AX 20)")
"consider not analyzed reads as clones, taking for junction the complete sequence, to be used on very small datasets (for example --not-analyzed-as-clones --all -X 20)")
-> group(group) -> level();
......@@ -855,7 +855,7 @@ int main (int argc, char **argv)
if (max_clones == NO_LIMIT_VALUE || max_clones > WARN_MAX_CLONES)
{
cout << endl
<< "* WARNING: " << PROGNAME << " was run with '-A' option or with a large '-z' option" << endl ;
<< "* WARNING: " << PROGNAME << " was run with '--all' option or with a large '--max-designations/-z' option" << endl ;
}
if (command == CMD_SEGMENT)
......@@ -1335,7 +1335,7 @@ int main (int argc, char **argv)
if (sort_clones.size() == 0)
{
cout << " ! No clones with current parameters." << endl;
cout << " ! See the 'Limits to report a clone' options (-r, --ratio, -z, -A)." << endl;
cout << " ! See the 'Limits to report and to analyze clones' options (-r, --min-ratio, -z, --all)." << endl;
}
else
{
......
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