fix full.aln to have correct VARIANT count when running snippy-core #531
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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.alnin thePREFIX.txtfile (VARIANT column) according to README:ATGCatgcCode change
The loop to lowercase variants of all samples won't be broken when the site is found not core