ui fix, api param

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

truvari/comparisons.py

@@ -258,14 +258,16 @@ 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
 
     :param `entry1`: First entry
     :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)