HGVS issue counsyl#61 - Reference HGVS without reference base leads t…

…o wrong coordinates and reference allele as it treats last digit as ref digit multiplying N that many times
SACGF · Dec 9, 2021 · 12924f0 · 12924f0
1 parent a0a8edd
commit 12924f0
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diff --git a/pyhgvs/models/hgvs_name.py b/pyhgvs/models/hgvs_name.py
@@ -128,6 +128,7 @@ class HGVSRegex(object):
     # cDNA allele syntax
     CDNA_ALLELE = [
         # No change
+        CDNA_START + EQUAL,
         CDNA_START + DNA_REF + EQUAL,
 
         # Substitution
@@ -189,6 +190,7 @@ class HGVSRegex(object):
     # Genomic allele syntax
     GENOMIC_ALLELE = [
         # No change
+        COORD_START + EQUAL,
         COORD_START + DNA_REF + EQUAL,
 
         # Substitution

diff --git a/pyhgvs/tests/test_hgvs_names.py b/pyhgvs/tests/test_hgvs_names.py
@@ -358,6 +358,18 @@ def test_invalid_coordinates():
          'mutation_type': '=',
      }),
 
+    # cDNA no change, no provided base
+    ('BRCA1:c.101=', True,
+     {
+         'gene': 'BRCA1',
+         'kind': 'c',
+         'cdna_start': CDNACoord(101),
+         'cdna_end': CDNACoord(101),
+         'ref_allele': '',
+         'alt_allele': '',
+         'mutation_type': '=',
+     }),
+
     # cDNA 1bp mutations.
     ('BRCA1:c.101A>C', True,
      {
@@ -542,6 +554,18 @@ def test_invalid_coordinates():
          'mutation_type': '=',
      }),
 
+    # Genomic no change + no ref base
+    ('BRCA1:g.101=', True,
+     {
+         'gene': 'BRCA1',
+         'kind': 'g',
+         'start': 101,
+         'end': 101,
+         'ref_allele': '',
+         'alt_allele': '',
+         'mutation_type': '=',
+     }),
+
     # Genomic 1bp mutations.
     ('BRCA1:g.101A>C', True,
      {