From 33fefab6cabc31998c3de46bc0b2bccfb5007a43 Mon Sep 17 00:00:00 2001
From: Adam English <ACEnglish@gmail.com>
Date: Sun, 7 Jan 2024 01:19:20 -0500
Subject: [PATCH] test fix

---
 truvari/__init__.py    | 2 --
 truvari/comparisons.py | 7 +------
 truvari/matching.py    | 4 ++--
 3 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/truvari/__init__.py b/truvari/__init__.py
index 108a2543..05ed6b5a 100644
--- a/truvari/__init__.py
+++ b/truvari/__init__.py
@@ -51,7 +51,6 @@
 :meth:`chunker`
 :meth:`cmd_exe`
 :meth:`consolidate_phab_vcfs`
-:meth:`coord_distance`
 :meth:`count_entries`
 :meth:`file_zipper`
 :meth:`help_unknown_cmd`
@@ -102,7 +101,6 @@
 )
 
 from truvari.comparisons import (
-    coord_distance,
     create_pos_haplotype,
     entry_boundaries,
     entry_distance,
diff --git a/truvari/comparisons.py b/truvari/comparisons.py
index d4bb8d08..7dd9d3b8 100644
--- a/truvari/comparisons.py
+++ b/truvari/comparisons.py
@@ -82,14 +82,9 @@ def entry_distance(entryA, entryB):
     """
     astart, aend = entry_boundaries(entryA)
     bstart, bend = entry_boundaries(entryB)
-    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):
     """
     Compare the genotypes of two entries
diff --git a/truvari/matching.py b/truvari/matching.py
index 2af80faf..67a13803 100644
--- a/truvari/matching.py
+++ b/truvari/matching.py
@@ -223,7 +223,7 @@ 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.reciprocal_overlap(bstart, bend, cstart, cend)
+        ret.ovlpct = truvari.entry_reciprocal_overlap(base, comp)
         if ret.ovlpct < self.params.pctovl:
             logging.debug("%s and %s overlap percent is too low (%.3f)",
                           str(base), str(comp), ret.ovlpct)
@@ -243,7 +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.st_dist, ret.ed_dist = bstart - cstart, bend - cend
         ret.calc_score()
 
         return ret