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

@@ -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
 

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='')