fix regression in input subsystem

Link: http://biosal.s3.amazonaws.com/quality-assurance-department/2014-08-13-03:01:01.log
Link: https://github.com/GeneAssembly/biosal/issues/549
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
add a seek test program

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>