From 2e317b69e5c5457770688f455982db510a5b4fc3 Mon Sep 17 00:00:00 2001
From: Jeremy Arbesfeld <jarbesfeld@gmail.com>
Date: Wed, 23 Oct 2024 10:22:07 -0400
Subject: [PATCH] Allow mapping to continue when intronic variants are found

---
 src/dcd_mapping/lookup.py  | 8 ++++++--
 src/dcd_mapping/vrs_map.py | 2 ++
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/dcd_mapping/lookup.py b/src/dcd_mapping/lookup.py
index 540ae0e..4905f25 100644
--- a/src/dcd_mapping/lookup.py
+++ b/src/dcd_mapping/lookup.py
@@ -489,7 +489,7 @@ def get_sequence(
 # -------------------------------- VRS-Python -------------------------------- #
 
 
-def translate_hgvs_to_vrs(hgvs: str) -> Allele:
+def translate_hgvs_to_vrs(hgvs: str) -> Allele | None:
     """Convert HGVS variation description to VRS object.
 
     :param hgvs: MAVE-HGVS variation string
@@ -500,7 +500,11 @@ def translate_hgvs_to_vrs(hgvs: str) -> Allele:
         hgvs = hgvs.replace(":c.", ":g.")
 
     tr = TranslatorBuilder(get_seqrepo())
-    allele: Allele = tr.translate_from(hgvs, "hgvs", do_normalize=False)
+    try:
+        allele: Allele = tr.translate_from(hgvs, "hgvs", do_normalize=False)
+    except ValueError as warn:
+        _logger.warning(warn)
+        return None
 
     if (
         not isinstance(allele.location, SequenceLocation)
diff --git a/src/dcd_mapping/vrs_map.py b/src/dcd_mapping/vrs_map.py
index 645df6b..5b9d884 100644
--- a/src/dcd_mapping/vrs_map.py
+++ b/src/dcd_mapping/vrs_map.py
@@ -393,6 +393,8 @@ def _get_variation(
     for hgvs_string in hgvs_strings:
         # Generate VRS Allele structure. Set VA digests and SL digests to None
         allele = translate_hgvs_to_vrs(hgvs_string)
+        if allele is None:
+            break
         allele.id = None
         allele.digest = None
         allele.location.id = None