lib/Crispr.pm
Added methods count_var_for_crRNA and
filter_crRNAs_from_target_by_snps_and_indels

t/crispr.t
Updated test file to test new methods

New Files: t/data/test.var.gz and t/data/test.var.gz.tbi
Test variation file and index for tests of new methods.
Filtering by SNPs
scripts/find_and_score_crispr_sites.pl
Added code to filter crispr target sites covering SNPs.
Added option for specifying variation file which turns on filtering when set.
Added Documentation for new option.
scripts/find_and_score_crispr_sites.pl
Uncommented code to insist on protein coding genes.
Need to do this better eventually. Could add option to allow non-coding genes.
Fixed bug that caused script to exit if gene object was undefined
when scoring crispr for 5' position.
Updated Documentation.