Grey genotypes

Fixed a bug where variants of low genotype quality (QUAL) were being filtered out (by --minqual) but not being masked from the alignment. This meant these sites would assume the default reference allelle, but often were low QUAL due to strand bias and other problems.

It only really affects people using snippy-core and will not change the SNPs you would call, but will affect the final core genome you get from a set of isolates. This is a significant change in some cases, hence the bump to 4.1.0

Thank you to @kmeaton for alerting me to this problem.