Unverified Commit ec9bba93 authored by Redmar van den Berg's avatar Redmar van den Berg Committed by GitHub

Merge pull request #1 from LUMC/devel

parents 72dae189 70d3ac7f
Pipeline #2855 passed with stage
in 2 minutes and 4 seconds
......@@ -154,6 +154,8 @@ Options:
called multiple times [required]
-ps, --positive-samples TEXT Sample(s) in positive-vcf to consider. May be
called multiple times [required]
-s, --stats PATH Path to output stats json file
-dc, --discordant PATH Path to output discordant VCF file
--help Show this message and exit.
......@@ -31,11 +31,26 @@ from .gcoverage import RefRecord, region_coverages
help="Sample(s) in positive-vcf to consider. "
"May be called multiple times",
def evaluate_cli(call_vcf, positive_vcf, call_samples, positive_samples):
@click.option("-s", "--stats", type=click.Path(writable=True),
help="Path to output stats json file", default='-')
@click.option("-dc", "--discordant", type=click.Path(writable=True),
help="Path to output discordant VCF file",
def evaluate_cli(call_vcf, positive_vcf, call_samples, positive_samples, stats,
c_vcf = VCF(call_vcf, gts012=True)
p_vcf = VCF(positive_vcf, gts012=True)
evaluated = site_concordancy(c_vcf, p_vcf, call_samples, positive_samples)
st, disc = site_concordancy(c_vcf, p_vcf, call_samples,
# Write the stats json file
with click.open_file(stats, 'w') as fout:
print(json.dumps(st), file=fout)
# If specified, write the discordant variants
if discordant:
with click.open_file(discordant, 'w') as fout:
for record in disc:
print(record, file=fout, end='')
......@@ -60,6 +60,8 @@ def site_concordancy(call_vcf: VCF,
"alleles_no_call": 0,
"alleles_low_qual": 0
discordant_count = 0
discordant_records = list()
for pos_record in positive_vcf:
d['total_sites'] += 1
query_str = "{0}:{1}-{2}".format(
......@@ -130,4 +132,9 @@ def site_concordancy(call_vcf: VCF,
# the same has no call in one or more of the VCF files
d['alleles_no_call'] += 2
return d
# The current variant is discordant
if d['alleles_discordant'] > discordant_count:
discordant_count = d['alleles_discordant']
return d, discordant_records
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