improved handling of plink options

Reworked command line options for partition-*.pl scripts to be less bulky.  Now an external file is used for plink options common to each partition and the perl module FetchOptions.pm will handle reading those.  New command line options are described in the help sections, e.g.,

  partition-snps-genome.pl --help

Also fixed a few issues with the run-plink.template file.

Changes to be committed:
	new file:   FetchOptions.pm
	modified:   partition-snps-by-chromosome.pl
	modified:   partition-snps-genome.pl
	new file:   plink-options
	modified:   run-plink.template