Update min-depth to integer

In the VCF files generated by GATK, DP is an integer, while the GQ field
holds a float.

 ##FORMAT=<ID=DP,Number=1,Type=Integer
 ##FORMAT=<ID=GQ,Number=1,Type=Float

README.md

@@ -161,7 +161,7 @@ Options:
   -s, --stats PATH              Path to output stats json file
   -dc, --discordant PATH        Path to output discordant VCF file
   -mq, --min-qual FLOAT         Minimum quality of variants to consider
-  -md, --min-depth FLOAT        Minimum depth of variants to consider
+  -md, --min-depth INTEGER      Minimum depth of variants to consider
   --help                        Show this message and exit.
 ```
 

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):