Merge testing into master

van den Bergrequested to merge
testing into devel

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/A vs 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
Edited by van den Berg

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