Merge pull request #65 from ramprasadn/master

Fix argument mismatch

Author: J35P312

setup.py

@@ -19,7 +19,7 @@
     ext_modules = []
 
 setup(name='svdb',
-      version='2.8.0',
+      version='2.8.1',
       url="https://github.com/J35P312/SVDB",
       author="Jesper Eisfeldt",
       author_email="jesper.eisfeldt@scilifelab.se",

svdb/__main__.py

@@ -36,16 +36,17 @@ def make_query_calls (args, queries, keyword):
                     args.query_vcf = output_file
         else:
             print("please ensure that both count and frequency tags are specified for all samples")
+    elif len(queries) > 1 and not args.prefix:
+        print("ERROR: Please provide a prefix")
+        quit()
+    elif len(queries) == 1 and args.prefix:
+        output_file  = args.prefix + "_query.vcf"    
+        query_module.main(args, output_file)
     else:
-        if args.prefix:
-            output_file  = args.prefix + "_query.vcf"    
-        else:
-            output_file=None
-
-        query_module.main(args,output_file)
+        query_module.main(args)
 
 def main():
-    version = "2.8.0"
+    version = "2.8.1"
     parser = argparse.ArgumentParser(
         """SVDB-{}, use the build module to construct databases, use the query module to query the database usign vcf files, or use the hist module to generate histograms""".format(version), add_help=False)
     parser.add_argument('--build', help="create a db",

svdb/query_module.py

@@ -8,7 +8,7 @@
 from . import database, overlap_module, readVCF
 
 
-def main(args, output_file):
+def main(args, output_file=None):
     # start by loading the variations
     queries = []
     if args.prefix: