fix full.aln to have correct VARIANT count when running snippy-core

[hsnguyen]

Output

This wouldn't affect core genome alignment or anything case-insensitive downstream from running snippy-core, just want to have correct count of variant sites from the .full.aln in the PREFIX.txt file (VARIANT column) according to README:

Character	Meaning
ATGC	Same as the reference
atgc	Different from the reference

Code change

The loop to lowercase variants of all samples won't be broken when the site is found not core