Cylinder collision shape not matching geometry

I’m trying model the growth of a tree like structure.Growing branches do not have a rigid body control due to the lack of scaling for cylinder collision shapes.

When a branch finishes growing I attempt to then replace that branch with a new brach/cylinder which has a rigid body control and collision shape.

The question is why is the collision shape incorrectly placed?. I checked that the debugger was not just drawing the collision shape incorrectly which was not the case.

 // g = growing branches geometry  
 // c = growing branches cylinder shape
 Vector3f localTransform = g.getLocalTranslation();
 Cylinder solidCylinder = new Cylinder(10,10,c.getRadius(),gHeight,true);
 Geometry solidGeom = new Geometry(g.getName()+"solid",solidCylinder);

 cylinderCol  =  new CylinderCollisionShape(new Vector3f(c.getRadius(),gHeight/2,c.getRadius()),1);    
 cylinderPhys = new RigidBodyControl(cylinderCol,1f);
 cylinderPhys.setPhysicsRotation(gRotate);// growing branches current rotation

Help is greatly appreciated

Perhaps you should not create the cylinder along the Y-axis, maybe the rotation you have assumes Z-axis as back-forward and then rotate. (just guessing but easy to try I guess)

Haha that was it thank you!