track total genotyping iterations, change iteration defaults
resolve targeting issue

The last position in a region was being excluded.  This ensures that the
entire target is processed.  The documentation is updated to reflect
this change.  scripts/fasta_generate_regions.py will now make completely
covering regions.
change to help text to reflect region spec change
use of big number library for improved numerical precision (ttmath)

Removes the QUAL limit of 50000, more experimentation may be required to
apply the method to the marginal genotype quality calculations.