Merge branch 'feat/vcfanno' into dev

cravat/oc.py

@@ -4,7 +4,9 @@
 from cravat.cravat_test import parser as test_parser
 from cravat.cravat_web import parser as gui_parser
 from cravat.cravat_report import parser as report_parser
+from cravat.vcfanno import vcfanno
 import sys
+from pathlib import Path
 
 root_p = argparse.ArgumentParser(
     description="Open-CRAVAT genomic variant interpreter. https://github.com/KarchinLab/open-cravat"
@@ -225,6 +227,23 @@
     help="Send feedback to the developers",
 )
 
+# vcfanno
+vcfanno_p = root_sp.add_parser(
+    'vcfanno',
+    help = 'annotate a vcf',
+)
+vcfanno_p.add_argument('input_path')
+vcfanno_p.add_argument('-a','--annotators',
+					   nargs = '*',
+)
+vcfanno_p.add_argument('-t','--threads',
+                       type = int,
+                       help = 'Number of CPU threads to use')
+vcfanno_p.add_argument('--temp-dir',
+                       type = Path,
+                       default = Path('temp-vcfanno'),
+                       help = 'Temporary directory for working files')
+vcfanno_p.set_defaults(func=vcfanno)
 
 def main():
     try: