report input VCF locations even when there is no data (or data for a while)

In the previous commit, if there were no reads for > CACHED_HAPLOTYPE_...
window size the input variants would not be updated and thus no report would be
produced at loci without data.  This resolves the problem by updating the
cached input variants at every new position.
remove issue with previous commit

Crash when not using variant input alleles.  Add a check and bail out if this
is the case.