Make --case|--controls|--refr args mandatory for simlike command

The `kevlar simlike` command supports an arbitrary number of VCF files as input. As a consequence, it's impossible to support the --case, --controls, and --refr arguments as positional arguments since --controls also supports an arbitrary number of values. The --case, --controls, and --refr settings are retained as option flags, but are now marked as mandatory. Closes #348.

kevlar/cli/simlike.py

@@ -9,25 +9,30 @@
 
 
 def subparser(subparsers):
-    """Define the `kevlar simlike` command-line interface."""
-
-    desc = "Sort variants by likelihood score"
-    subparser = subparsers.add_parser('simlike', description=desc,
-                                      add_help=False)
+    subparser = subparsers.add_parser(
+        'simlike', description='Sort variants by likelihood score',
+        add_help=False
+    )
 
     count_args = subparser.add_argument_group(
         'K-mer count files',
         'Likelihood scores are based on the abundance of alternate allele '
         'k-mers in each sample and on the abundance of reference allele '
         'k-mers in the reference genome.'
     )
-    count_args.add_argument('--case', metavar='CT',
-                            help='k-mer counttable for case/proband')
-    count_args.add_argument('--controls', nargs='+', metavar='CT',
-                            help='k-mer counttables for controls/parents/'
-                            'siblings, 1 counttable per sample')
-    count_args.add_argument('--refr', metavar='REFR', help='k-mer '
-                            'smallcounttable for reference genome')
+    count_args.add_argument(
+        '--case', metavar='CT', required=True,
+        help='k-mer counttable for case/proband'
+    )
+    count_args.add_argument(
+        '--controls', nargs='+', metavar='CT', required=True,
+        help='k-mer counttables for controls/parents/siblings, 1 counttable '
+        'per sample'
+    )
+    count_args.add_argument(
+        '--refr', metavar='REFR',  required=True,
+        help='k-mer smallcounttable for reference genome'
+    )
 
     thresh_args = subparser.add_argument_group(
         'K-mer count thresholds',