Fix tests

biocommons · Jan 23, 2024 · c9be9db · c9be9db
1 parent 1b28fa8
commit c9be9db
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/src/hgvs/utils/altseqbuilder.py b/src/hgvs/utils/altseqbuilder.py
@@ -342,10 +342,10 @@ def _setup_incorporate(self):
                 if pos.base < 0:  # 5' UTR
                     result = cds_start - 1
                 else:  # cds/intron
-                    if pos.offset <= 0:
-                        result = (cds_start - 1) + pos.base + pos.offset - 1
+                    if pos.offset < 0:
+                        result = (cds_start - 1) + pos.base - 2
                     else:
-                        result = (cds_start - 1) + pos.base
+                        result = (cds_start - 1) + pos.base - 1
             elif pos.datum == Datum.CDS_END:  # 3' UTR
                 result = cds_stop + pos.base - 1
             else:

diff --git a/tests/test_hgvs_assemblymapper.py b/tests/test_hgvs_assemblymapper.py
@@ -228,7 +228,7 @@ def test_map_of_dup_intron_exon_boundary_rc(self):
 
     def test_map_of_dup_exon_intron_boundary(self):
         hgvs_c = "NM_024529.4:c.131+1_131+3dup"
-        hgvs_p = "NP_078805.3:p.(Gly44_Thr45insVal)"
+        hgvs_p = "NP_078805.3:p.(Thr45Ter)"
 
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
         var_p = self.am.c_to_p(var_c)
@@ -237,7 +237,7 @@ def test_map_of_dup_exon_intron_boundary(self):
 
     def test_map_of_dup_exon_intron_boundary_rc(self):
         hgvs_c = "NM_004985.4:c.111+1_111+4dup"
-        hgvs_p = "NP_004976.2:p.(Asp38GlyfsTer11)"
+        hgvs_p = "NP_004976.2:p.(Asp38ValfsTer11)"
 
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
         var_p = self.am.c_to_p(var_c)