Assuming you don't want to change how your application handles meshes internally (i.e. switch from passing triangles to the pipeline to passing quads) the easiest solution is to alter your parser so that it creates two triangles in place of each quad.
For each face:
f v1 v2 v3 v4
You'll want to create two triangles: v1 v2 v4
and v4 v2 v3
.
Per vertex data like normals and texture coordinates will stay the same.