From 70d3ac7f18254f5289126f7f6537e425a05665d6 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Thu, 8 Aug 2019 08:59:59 +0200
Subject: [PATCH] Write stats to stdout by default
This is also the default behaviour in master. This change restores
the default behaviour, while still preserving the option to write
the stats json directly to a file by specifying --stats.
---
README.md | 6 +++---
vtools/cli.py | 6 +++---
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index 947346e..a998cd6 100644
--- a/README.md
+++ b/README.md
@@ -154,10 +154,10 @@ 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 [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
- ```
+ --help Show this message and exit.
+```
## License
diff --git a/vtools/cli.py b/vtools/cli.py
index 30cd698..77d54a7 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", required=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",
required=False)
@@ -43,12 +43,12 @@ def evaluate_cli(call_vcf, positive_vcf, call_samples, positive_samples, stats,
st, disc = site_concordancy(c_vcf, p_vcf, call_samples,
positive_samples)
# Write the stats json file
- with open(stats, 'w') as fout:
+ with click.open_file(stats, 'w') as fout:
print(json.dumps(st), file=fout)
# If specified, write the discordant variants
if discordant:
- with open(discordant, 'w') as fout:
+ with click.open_file(discordant, 'w') as fout:
for record in disc:
print(record, file=fout, end='')
--
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