From 8c9faf2b513fb148406dda561320660629ce1202 Mon Sep 17 00:00:00 2001
From: Brendan ODonnell <brendan@odonnell.xyz>
Date: Wed, 20 Dec 2023 15:19:01 -0500
Subject: [PATCH] Add tests for dups spanning boundary

---
 tests/data/cache-py3.hdp          | Bin 994870 -> 994960 bytes
 tests/test_hgvs_assemblymapper.py |  16 ++++++++++++++++
 tests/test_hgvs_variantmapper.py  |  10 ++++++++++
 3 files changed, 26 insertions(+)

diff --git a/tests/data/cache-py3.hdp b/tests/data/cache-py3.hdp
index e9b29e46356d1e5ce541fa0fdc1bd9133e635793..fc436e742b6e965f97a3d0c2bd9586964e5bd297 100644
GIT binary patch
delta 121
zcmdmX$7aG^n}!y~7N!>F7M2#)7Pc1l7LFFq7OocV7M>Q~7QQX~-^CdxZvP?9ZzCp}
z!K~RhMI&ok2?K+d<b@_~FBu>)T~Lo-Qjgi)-F*tO{I^>``5!<c%cq=yA<Gv?q;@3r
KFaed7>Hz?(IVdUs

delta 50
zcmbPm*Jj%tn}!y~7N!>F7M2#)7Pc1l7LFFq7OocV7M>Q~7QQX~-^CftxBn35w-IA1
G)dK*_6cBCz

diff --git a/tests/test_hgvs_assemblymapper.py b/tests/test_hgvs_assemblymapper.py
index 25953bf3..2942f035 100644
--- a/tests/test_hgvs_assemblymapper.py
+++ b/tests/test_hgvs_assemblymapper.py
@@ -201,6 +201,14 @@ def test_c_to_p_with_stop_gain(self):
         self.assertEqual(str(var_p), hgvs_p)
 
     def test_map_of_dup_intron_exon_boundary(self):
+        hgvs_c = "NM_024529.4:c.132-1_132dup"
+        hgvs_p = "NP_078805.3:p.?"
+
+        var_c = self.hp.parse_hgvs_variant(hgvs_c)
+        var_p = self.am.c_to_p(var_c)
+
+        self.assertEqual(str(var_p), hgvs_p)
+
         hgvs_c = "NM_024529.4:c.132-2_132-1dup"
         hgvs_p = "NP_078805.3:p.(Thr45GlyfsTer65)"
 
@@ -227,6 +235,14 @@ def test_map_of_dup_intron_exon_boundary_rc(self):
         self.assertEqual(str(var_p), hgvs_p)
 
     def test_map_of_dup_exon_intron_boundary(self):
+        hgvs_c = "NM_024529.4:c.130_131+1dup"
+        hgvs_p = "NP_078805.3:p.?"
+
+        var_c = self.hp.parse_hgvs_variant(hgvs_c)
+        var_p = self.am.c_to_p(var_c)
+
+        self.assertEqual(str(var_p), hgvs_p)
+
         hgvs_c = "NM_024529.4:c.131+1_131+3dup"
         hgvs_p = "NP_078805.3:p.(Thr45Ter)"
 
diff --git a/tests/test_hgvs_variantmapper.py b/tests/test_hgvs_variantmapper.py
index a28fdfc5..704301c0 100644
--- a/tests/test_hgvs_variantmapper.py
+++ b/tests/test_hgvs_variantmapper.py
@@ -131,6 +131,11 @@ def test_map_of_ins_exon_intron_boundary(self):
         self.assertEqual(str(var_p), "NP_004371.2:p.(Phe1085LeufsTer2)")
 
     def test_map_of_dup_intron_exon_boundary(self):
+        hgvs_c = "NM_024529.4:c.132-1_132dup"
+        var_c = self.hp.parse_hgvs_variant(hgvs_c)
+        var_p = self.vm.c_to_p(var_c)
+        self.assertEqual(str(var_p), "NP_078805.3:p.?")
+
         hgvs_c = "NM_024529.4:c.132-2_132-1dup"
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
         with self.assertRaises(HGVSError):
@@ -148,6 +153,11 @@ def test_map_of_dup_intron_exon_boundary_rc(self):
             var_p = self.vm.c_to_p(var_c)
 
     def test_map_of_dup_exon_intron_boundary(self):
+        hgvs_c = "NM_024529.4:c.130_131+1dup"
+        var_c = self.hp.parse_hgvs_variant(hgvs_c)
+        var_p = self.vm.c_to_p(var_c)
+        self.assertEqual(str(var_p), "NP_078805.3:p.?")
+
         hgvs_c = "NM_024529.4:c.131+1_131+3dup"
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
         with self.assertRaises(HGVSError):