Commit e0133fae authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: dump config into .vidjil

There is now some hack to get a json, it could be improved.
See #3837.
parent 1fd605f6
...@@ -230,6 +230,7 @@ int main (int argc, char **argv) ...@@ -230,6 +230,7 @@ int main (int argc, char **argv)
#endif #endif
CLI::App app{"# vidjil-algo -- V(D)J recombinations analysis", argv[0]}; CLI::App app{"# vidjil-algo -- V(D)J recombinations analysis", argv[0]};
app.config_formatter(std::make_shared<ConfigJSON>());
app.get_formatter()->label("REQUIRED", ""); app.get_formatter()->label("REQUIRED", "");
app.get_formatter()->label("Positionnals", ""); app.get_formatter()->label("Positionnals", "");
app.failure_message(failure_message_doc); app.failure_message(failure_message_doc);
...@@ -744,6 +745,9 @@ int main (int argc, char **argv) ...@@ -744,6 +745,9 @@ int main (int argc, char **argv)
} }
cout << endl; cout << endl;
// Dump configuration
json j_config = json::parse(app.config_to_str(true, true));
////////////////////////////////// //////////////////////////////////
// Display time and date // Display time and date
time_t rawtime; time_t rawtime;
...@@ -1557,6 +1561,7 @@ int main (int argc, char **argv) ...@@ -1557,6 +1561,7 @@ int main (int argc, char **argv)
// Complete main output // Complete main output
output.set("config", j_config);
output.set("diversity", jsonDiversity); output.set("diversity", jsonDiversity);
output.set("samples", "log", { stream_segmentation_info.str() }) ; output.set("samples", "log", { stream_segmentation_info.str() }) ;
output.set("reads", { output.set("reads", {
......
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