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/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

added 5 commits

• d6779d59 - tox automatically calls pip install '.'
• 3c789431 - Update min-depth to integer
• 257600ce - Write to stats file instead of using print
• e62c9164 - Use get_header_type to determine if RGQ is present
• e6309163 - The discordant VCF file is gzipped

Compare with previous version

resolved all threads

changed the description

changed target branch from master to devel

merged

mentioned in commit 335925d5