report invalid edges as warnings instead of errors

Also, report a warning only once for each faulty edge.

Reported-by: Patrick Laffy <P.Laffy@aims.gov.au>
Link: http://comments.gmane.org/gmane.science.biology.ray-genome-assembler/724
Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>