Merge testing into master
Various changes required for the new harmony pipeline. The most important changes are listed below:
- Add testing, including various tests to make sure the program aborts on unsupported input
- Change the way the vcf files are compared to allow comparisons between different REF/ALT values
- Add support for comparing partial calls, e.g.
A/.is counted as 1 concordant allele, and 1 'no call'
- Add support for filtering on RGQ instead of GQ when a site is called as homref
- Write discordant variants from the 'call' VCF file to a valid VCF file