pooled frequency-based calling (and nan guard)

Separate --pooled into --pooled-discrete (old behavior) and
--pooled-continuous.  In the continuous case, allele observation
characteristics are reported for all alleles which passed the input
filters (default -F 0.2 -C 2).  Pooled continuous calling does not
modify the Bayesian algorithm, and is effectively orthogonal to other
parameters.

For instance, --pooled-discrete and --pooled-continuous can be specified
toether.  The called genotypes will be affected by the --ploidy setting
and --pooled-discrete flags, but the output will reflect all observed
alleles passing input filters a the site.

Also, guard against nan's in output (Utility.cpp).
version 0.9.9, set as default "mappability" priors

freebayes can estimate the probability that the loci in question is
accurately mapped using a number of features extracted from read
placement and distribution among samples.

This framework effectively extends the basic Bayesian formulation from
P(genotypes | reads) to P(genotypes, properly-mapped alleles | reads).
As such, the QUAL value must be understood to incorporate expectations
about mappability derived from observation features such as allele
balance, strand bias, and read placement relative to the allele.

This commit sets this model on by default.

To turn OFF this behavior, use -wVa or:
    --hwe-priors-off \
    --binomial-obs-priors-off \
    --allele-balance-priors-off

Extensive testing showed that this combination of parameters provided
excellent sensitivity and specificity at all levels of genomic coverage
and numbers of samples.  The largest improvement in performance is for
low-coverage resequencing (<5x coverage, >1000 samples) experiments.
Higher-coverage experiments, where data tends to overwhelm priors,
should not be affected.