diff --git a/truvari/annotations/chunks.py b/truvari/annotations/chunks.py index a303ca5..107a07a 100644 --- a/truvari/annotations/chunks.py +++ b/truvari/annotations/chunks.py @@ -24,9 +24,9 @@ def parse_args(args): parser.add_argument("-c", "--chunksize", type=int, default=500, help="Distance between variants to split chunks (%(default)s)") parser.add_argument("-s", "--sizemin", type=int, default=50, - help="Minimum SV length") + help="Minimum SV length (%(default)s)") parser.add_argument("-S", "--sizemax", type=int, default=50000, - help="Maximum SV length") + help="Maximum SV length (%(default)s)") args = parser.parse_args(args) truvari.setup_logging(show_version=True) return args diff --git a/truvari/comparisons.py b/truvari/comparisons.py index e3956d8..ddb8110 100644 --- a/truvari/comparisons.py +++ b/truvari/comparisons.py @@ -258,7 +258,7 @@ def entry_seq_similarity(entryA, entryB, ref=None, min_len=0): return max(unroll_compare(a_seq, b_seq, st_dist), unroll_compare(b_seq, a_seq, -st_dist), seqsim(a_seq, b_seq)) -def entry_reciprocal_overlap(entry1, entry2): +def entry_reciprocal_overlap(entry1, entry2, ins_inflate=True): """ Calculates reciprocal overlap of two entries @@ -266,6 +266,8 @@ def entry_reciprocal_overlap(entry1, entry2): :type `entry1`: :class:`pysam.VariantRecord` :param `entry2`: Second entry :type `entry2`: :class:`pysam.VariantRecord` + :param `ins_inflate`: inflate entry boundaries + :type `ins_inflate`: bool :return: The reciprocal overlap :rtype: float @@ -279,8 +281,8 @@ def entry_reciprocal_overlap(entry1, entry2): >>> truvari.entry_reciprocal_overlap(a, b) 0 """ - astart, aend = entry_boundaries(entry1, True) - bstart, bend = entry_boundaries(entry2, True) + astart, aend = entry_boundaries(entry1, ins_inflate) + bstart, bend = entry_boundaries(entry2, ins_inflate) return reciprocal_overlap(astart, aend, bstart, bend)