From f7845a91791fda4124e943c3f40cde5f4fd42380 Mon Sep 17 00:00:00 2001 From: Adam English Date: Sat, 4 Jan 2025 23:24:22 -0500 Subject: [PATCH] bnd progress allow bnd to be turned off. stop bnd from breaking collapse --- truvari/bench.py | 7 ++++--- truvari/matching.py | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/truvari/bench.py b/truvari/bench.py index 05deeb91..b74071cc 100644 --- a/truvari/bench.py +++ b/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): diff --git a/truvari/matching.py b/truvari/matching.py index c8a5140c..9880c97f 100644 --- a/truvari/matching.py +++ b/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