output proper error message on malformed input data

This addresses an issue reported on the GenomeTools mailing list (http://genometools.org/pipermail/gt-users/2013-December/000673.html) where an error in the input files failed to generate a sensible error message. Since the input options have been changed for 1.5.2 but still allow this 'old-style' input for compatibility reasons I fixed this problem.