core/output.{h,cpp}: VidjilOuput, with_clones option

see #3861

algo/core/output.cpp

@@ -129,10 +129,11 @@ CloneOutput* SampleOutput::getClone(junction junction)
 
 // .vidjil json output
 
-void SampleOutputVidjil::out(ostream &s)
+void SampleOutputVidjil::out(ostream &s, bool with_clones)
 {
    json j_clones;
 
+   if (with_clones)
    for (auto it: clones)
       j_clones.push_back(it.second->toJson());
 

algo/core/output.h

@@ -69,7 +69,7 @@ public:
 class SampleOutputVidjil : public SampleOutput
 {
 public:
-  void out(ostream &s);
+  void out(ostream &s, bool with_clones=true);
 };
 
 // AIRR