Somatic SNV caller using base and alignment qualities

This is the SNV caller that I am been working on for the ICGC-TCGA challenge, I wanted to finally get this into master so that others could work on it as well and make additions/alterations.  Also I think this may have hit its peak of how well it can do so, I wanted to start working on some different ideas, but wanted this as base to work from or improve on.