Merge pull request #76 from oxfordmmm/fix/allow-vcf-overlaps

fix: bump gumpy to allow vcf overlaps
oxfordmmm · Jul 8, 2024 · 952e1dd · 952e1dd
2 parents 16678ab + 21c15b1
commit 952e1dd
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Showing 4 changed files with 7 additions and 6 deletions.
diff --git a/bin/merge-vcfs b/bin/merge-vcfs
@@ -23,11 +23,12 @@ def fetch_minos_positions(minos_vcf: Path) -> set[int]:
             positions.add(pos)
         else:
             # Check if the indel is a deletion or insertion (deleted bases need excluding too)
-            call, bases = vcf.calls[(pos, m_type)]["call"]
-            if call == "ins":
-                positions.add(pos)
-            else:
-                positions.update(range(pos, pos + len(bases)))
+            for item in vcf.calls[(pos, m_type)]:
+                call, bases = item["call"]
+                if call == "ins":
+                    positions.add(pos)
+                else:
+                    positions.update(range(pos, pos + len(bases)))
     return positions
 
 

diff --git a/setup.cfg b/setup.cfg
@@ -16,7 +16,7 @@ package_dir =
 packages = find:
 python_requires = >=3.10
 install_requires = 
-    gumpy>=1.3.3
+    gumpy>=1.3.4
     piezo>=0.8.3
     vcf_subset>=1.1.2
     numpy

diff --git a/tests/test-cases/TEST-DNA-no-overlap.gbk.pkl b/tests/test-cases/TEST-DNA-no-overlap.gbk.pkl
diff --git a/tests/test-cases/TEST-DNA.gbk.pkl b/tests/test-cases/TEST-DNA.gbk.pkl