Commit 828d7e09 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: --no-vidjil

see #3861
parent 39109911
......@@ -582,6 +582,8 @@ int main (int argc, char **argv)
app.add_option("--dir,-o", out_dir, "output directory", true) -> group(group) -> type_name("PATH");
app.add_option("--base,-b", f_basename, "output basename (by default basename of the input file)") -> group(group) -> type_name("STRING");
bool no_vidjil = false;
app.add_flag("--no-vidjil", no_vidjil, "do not output .vidjil") -> group(group) -> level();
int verbose = 0 ;
app.add_flag_function("--verbose,-v", [&](size_t n) { verbose += n ; }, "verbose mode") -> group(group);
......@@ -1739,11 +1741,19 @@ int main (int argc, char **argv)
static_cast<SampleOutputAIRR *>(&output) -> out(out_airr);
//$ Output .vidjil json
cout << " ==> " << f_json << "\t(data file for the Vidjil web application)" << endl ;
cout << " ==> " << f_json ;
if (no_vidjil)
{
cout << "\t(data file for the Vidjil web application)" << endl;
}
else
{
cout << "\t(only metadata, no clone output)" << endl;
}
ofstream out_json(f_json.c_str()) ;
SampleOutputVidjil *outputVidjil = static_cast<SampleOutputVidjil *>(&output);
outputVidjil->out(out_json);
outputVidjil -> out(out_json, !no_vidjil);
//$$ Clean
if (__only_on_exit__clean_memory) { delete multigermline ; delete reads; } return 0 ;
......
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