Commit 3c789431 authored by van den Berg's avatar van den Berg
Browse files

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
parent d6779d59
......@@ -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.
```
......
......@@ -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):
......
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