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

@@ -35,11 +35,11 @@ from .gcoverage import RefRecord, region_coverages
 @click.option("-s", "--stats", type=click.Path(writable=True),
               help="Path to output stats json file")
 @click.option("-dvcf", "--discordant-vcf", type=click.Path(writable=True),
-              help="Path to output discordant VCF file",
+              help="Path to output gzipped discordant vcf file",
               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):
@@ -52,7 +52,7 @@ def evaluate_cli(call_vcf, positive_vcf, call_samples, positive_samples,
         print(json.dumps(st))
     else:
         with click.open_file(stats, 'w') as fout:
-            print(json.dumps(st), file=fout)
+            fout.write(json.dumps(st))
 
     # If there were discordand records, and a discordant-vcf should be written
     if len(disc) > 0 and discordant_vcf: