pylint fix

truvari/bench.py

@@ -585,9 +585,9 @@ def build_matrix(self, base_variants, comp_variants, chunk_id=0, skip_gt=False,
         for bid, base in enumerate(base_variants):
             base_matches = []
             for cid, comp in enumerate(comp_variants):
-                mat = matcher(base, comp, 
+                mat = matcher(base, comp,
                               matid=[f"{chunk_id}.{bid}", f"{chunk_id}.{cid}"],
-                              skip_gt=skip_gt, 
+                              skip_gt=skip_gt,
                               short_circuit=self.short_circuit)
                 logging.debug("Made mat -> %s", mat)
                 base_matches.append(mat)

truvari/matching.py

@@ -263,20 +263,16 @@ def bnd_build_match(self, base, comp, matid=None, **_kwargs):
         """
         Build a MatchResult for bnds
         """
-        def bounds(entry, pos, key='POS'):
+        def bounds(pos):
             """
-            Inflate a bnd position
-            """
-            start = pos - self.params.bnddist
-            end = pos + self.params.bnddist
-
-            """ Experimental, but it's getting tricky, so need clarification
+            Inflate a bnd position based on CIPOS. 
+            Experimental, but it's getting tricky, so need clarification
             For example, why does GIAB use CIPOS1 instead of the standard CIPOS? (not to mention Type=String).
             Also, I assumed that the CIPOS was ±POS, but it seems like the standard is that the ambiguity is between 
             POS, POS+CIPOS[0]. But then, there is no enforcement of strands with CIPOS, I think, so it could always be 
             positive and if it's a complement BND it might need POS - CIPOS? 
             I'm dropping for now
-
+            entry and key were also parameters
             key = 'CI' + key
             idx = 0 if key == 'POS' else 1
             if key in entry.info: # Just CIPOS
@@ -292,6 +288,9 @@ def bounds(entry, pos, key='POS'):
                     if k not in [None, '.']:
                         end += int(k)
             """
+            start = pos - self.params.bnddist
+            end = pos + self.params.bnddist
+
             return start, end
 
         ret = truvari.MatchResult()
@@ -301,7 +300,7 @@ def bounds(entry, pos, key='POS'):
         ret.matid = matid
         ret.state = base.chrom == comp.chrom
         ret.st_dist = base.pos - comp.pos
-        ret.state &= truvari.overlaps(*bounds(base, base.pos, 'POS'), *bounds(comp, comp.pos, 'POS'))
+        ret.state &= truvari.overlaps(*bounds(base.pos), *bounds(comp.pos))
         b_bnd = bnd_direction_strand(base.alts[0])
         c_bnd = bnd_direction_strand(comp.alts[0])
         ret.state &= b_bnd == c_bnd
@@ -311,7 +310,7 @@ def bounds(entry, pos, key='POS'):
         ret.ed_dist = b_pos2[1] - c_pos2[1]
         ret.state &= b_pos2[0] == c_pos2[0]
 
-        ret.state &= truvari.overlaps(*bounds(base, b_pos2[1], 'END'), *bounds(comp, c_pos2[1], 'END'))
+        ret.state &= truvari.overlaps(*bounds(b_pos2[1]), *bounds(c_pos2[1]))
         ret.state &= ret.ed_dist < self.params.bnddist
 
         self.compare_gts(ret, base, comp)