avoid and resolve #6

Some aligners will place reads past the ends of short reference sequences that
aren't flanked by Ns.

Before this commit, freebayes would choke on this kind of issue, and say it was
"Unable to read reference sequence base past end of current reference
sequence."  Now, it just registers the error and continues, as it probably
always should have.
change behavior of --report-genotype-likelihood-max

This does not affect typical operation vs. the previous commit.