From e55c857793a9d340e200a5ff3cd6dbf878f3488f Mon Sep 17 00:00:00 2001
From: Matthew Colpus <mpcolpus@gmail.com>
Date: Fri, 15 Mar 2024 12:35:39 +0000
Subject: [PATCH] fix: only clash for different vcf rows

---
 gumpy/variantfile.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gumpy/variantfile.py b/gumpy/variantfile.py
index 21f76b3..d1ec4f0 100644
--- a/gumpy/variantfile.py
+++ b/gumpy/variantfile.py
@@ -567,14 +567,15 @@ def __find_calls(self):
                         calls.append((index + p, variant_type, metadata))
 
         # Convert calls to dict, checking for clashes
-        positions = set()
+        positions = {}
         self.calls = {}
         for pos, type_, metadata in calls:
             if pos in positions:
-                raise ValueError(
-                    "Multiple calls at position " + str(pos) + " in VCF file"
-                )
-            positions.add(pos)
+                if positions[pos] != metadata["original_vcf_row"]:
+                    raise ValueError(
+                        "Multiple calls at position " + str(pos) + " in VCF file"
+                    )
+            positions[pos] = metadata["original_vcf_row"]
             self.calls[(pos, type_)] = metadata
 
     def _simplify_call(self, ref: str, alt: str) -> List[Tuple[int, str, str]]: