From 51eb6db99836fb07c185b8542b19cfad53259b1a Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Tue, 22 Oct 2019 11:26:05 +0200
Subject: [PATCH] Do not use '-' as a stand in for stdout
---
vtools/cli.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/vtools/cli.py b/vtools/cli.py
index 7f95ef9..ac5c023 100644
--- a/vtools/cli.py
+++ b/vtools/cli.py
@@ -32,7 +32,7 @@ from .gcoverage import RefRecord, region_coverages
"May be called multiple times",
required=True)
@click.option("-s", "--stats", type=click.Path(writable=True),
- help="Path to output stats json file", default='-')
+ help="Path to output stats json file")
@click.option("-dc", "--discordant", type=click.Path(writable=True),
help="Path to output discordant VCF file",
required=False)
@@ -47,8 +47,11 @@ def evaluate_cli(call_vcf, positive_vcf, call_samples, positive_samples,
st, disc = site_concordancy(c_vcf, p_vcf, call_samples,
positive_samples, min_qual, min_depth)
# Write the stats json file
- with click.open_file(stats, 'w') as fout:
- print(json.dumps(st), file=fout)
+ if stats is None:
+ print(json.dumps(st))
+ else:
+ with click.open_file(stats, 'w') as fout:
+ print(json.dumps(st), file=fout)
# If specified, write the discordant variants
if discordant:
--
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