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

vtools/cli.py

@@ -39,7 +39,7 @@ from .gcoverage import RefRecord, region_coverages
               required=False)
 @click.option("-mq", "--min-qual", type=float,
               help="Minimum quality of variants to consider", default=30)
-@click.option("-md", "--min-depth", type=float,
+@click.option("-md", "--min-depth", type=int,
               help="Minimum depth of variants to consider", default=0)
 def evaluate_cli(call_vcf, positive_vcf, call_samples, positive_samples,
                  min_qual, min_depth, stats, discordant_vcf):