SNP predictor settings need fine-tuning

[RobJackson28]

Our default settings need fine-tuning, or we need to allow user the option (eventually) to fine-tune the settings and filter SNPs based on their p-value (lower number = higher confidence that it is real). One example where a SNP is not being identified (false-negative) is with L6R2, where there should be two SNPs: G145T and C335T, but only one is predicted. On the other side of this issue is that too lenient of settings will result in false-positive SNPs being predicted erroneously.

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[RobJackson28]

@chgibb Also, SNPs shouldn't necessarily always be predicted (as this may not be a part of a workflow). The user should have the option to add SNP prediction either during the alignment setup or if possible, in the post-alignment results, in the Pathogen window.