bnd progress

allow bnd to be turned off. stop bnd from breaking collapse

truvari/bench.py

@@ -60,8 +60,8 @@ def parse_args(args):
                         help="Number of matches reported per-call (%(default)s)")
     thresg.add_argument("--dup-to-ins", action="store_true",
                         help="Assume DUP svtypes are INS (%(default)s)")
-    thresg.add_argument("-B", "--bnddist", type=truvari.restricted_int, default=defaults.bnddist,
-                        help="Maximum distance allowed between BNDs")
+    thresg.add_argument("-B", "--bnddist", type=int, default=defaults.bnddist,
+                        help="Maximum distance allowed between BNDs (%(default)s; -1=off)")
     thresg.add_argument("-C", "--chunksize", type=truvari.restricted_int, default=defaults.chunksize,
                         help="Max reference distance to compare calls (%(default)s)")
 
@@ -520,7 +520,8 @@ def compare_chunk(self, chunk):
             chunk_dict["base"], chunk_dict["comp"], chunk_id)
         self.check_refine_candidate(result)
         # Check BNDs separately
-        result.extend(self.bnd_compare(chunk_dict['base_BND'], chunk_dict['comp_BND'], chunk_id))
+        if self.matcher.params.bnddist != -1:
+            result.extend(self.bnd_compare(chunk_dict['base_BND'], chunk_dict['comp_BND'], chunk_id))
         return result
 
     def compare_calls(self, base_variants, comp_variants, chunk_id=0):

truvari/matching.py

@@ -137,7 +137,7 @@ def make_match_params_from_args(args):
         ret.bSample = args.bSample if args.bSample else 0
         ret.cSample = args.cSample if args.cSample else 0
         ret.dup_to_ins = args.dup_to_ins if "dup_to_ins" in args else False
-        ret.bnddist = args.bnddist
+        ret.bnddist = args.bnddist if 'bnddist' in args else -1
         # filtering properties
         ret.sizemin = args.sizemin
         ret.sizefilt = args.sizefilt