code clean

might be a little faster to not call entry_boundaries multiple times

truvari/__init__.py

@@ -51,6 +51,7 @@
 :meth:`chunker`
 :meth:`cmd_exe`
 :meth:`consolidate_phab_vcfs`
+:meth:`coord_distance`
 :meth:`count_entries`
 :meth:`file_zipper`
 :meth:`help_unknown_cmd`
@@ -101,6 +102,7 @@
 )
 
 from truvari.comparisons import (
+    coord_distance,
     create_pos_haplotype,
     entry_boundaries,
     entry_distance,

truvari/comparisons.py

@@ -82,8 +82,13 @@ def entry_distance(entryA, entryB):
     """
     astart, aend = entry_boundaries(entryA)
     bstart, bend = entry_boundaries(entryB)
-    return astart - bstart, aend - bend
+    return coord_distance(astart, aend, bstart, bend)
 
+def coord_distance(astart, aend, bstart, bend):
+    """
+    Return start and end distances
+    """
+    return astart - bstart, aend - bend
 
 def entry_gt_comp(entryA, entryB, sampleA=None, sampleB=None):
     """

truvari/matching.py

@@ -223,15 +223,14 @@ def build_match(self, base, comp, matid=None, skip_gt=False, short_circuit=False
                 ret.comp_gt_count = sum(1 for _ in ret.comp_gt if _ == 1)
             ret.gt_match = abs(ret.base_gt_count - ret.comp_gt_count)
 
-        ret.ovlpct = truvari.entry_reciprocal_overlap(base, comp)
+        ret.ovlpct = truvari.reciprocal_overlap(bstart, bend, cstart, cend)
         if ret.ovlpct < self.params.pctovl:
             logging.debug("%s and %s overlap percent is too low (%.3f)",
                           str(base), str(comp), ret.ovlpct)
             ret.state = False
             if short_circuit:
                 return ret
 
-        ret.st_dist, ret.ed_dist = truvari.entry_distance(base, comp)
         if self.params.pctseq > 0:
             ret.seqsim = truvari.entry_seq_similarity(
                 base, comp, self.reference, self.params.minhaplen)
@@ -244,6 +243,7 @@ def build_match(self, base, comp, matid=None, skip_gt=False, short_circuit=False
         else:
             ret.seqsim = 0
 
+        ret.st_dist, ret.ed_dist = truvari.coord_distance(bstart, bend, cstart, cend)
         ret.calc_score()
 
         return ret