Report the location on error

CHANGELOG.rst

@@ -26,6 +26,8 @@ Novel module
 Bugfixes
 ========
 * Fix a rare bug where different modules use the same multiqc file list.
+* Fix a bug with filtering VEP records that contain multiple population
+  frequency records for a single variant.
 
 Updates
 =======

includes/snv-indels/scripts/filter_vep.py

@@ -119,11 +119,13 @@ def _extract_frequencies(self) -> FrequenciesType:
                 if not frequencies:
                     frequencies = var["frequencies"]
                 elif var["frequencies"] != frequencies:
-                    msg = "Multiple colocated variants with 'frequencies' entry encountered"
+                    location = self.location
+                    msg = f"Multiple colocated variants with 'frequencies' entry encountered on {location}"
                     raise RuntimeError(msg)
 
         if len(frequencies) > 1:
-            msg = "'frequencies' entry from VEP should only contain a single key"
+            location = self.location
+            msg = f"'frequencies' entry with multiple keys encountered on {location}"
             raise RuntimeError(msg)
 
         return frequencies
@@ -162,6 +164,18 @@ def above_population_threshold(self, population: str, threshold: float) -> bool:
         """
         return self.population_frequency(population) > threshold
 
+    @property
+    def location(self) -> str:
+        """
+        Return a representation the location of the VEP record on the genome
+        """
+        input = self.get("input")
+        if input is None:
+            return "unknown location"
+
+        chrom, pos = input.split("\t")[:2]
+        return f"{chrom}:{pos}"
+
 
 def read_goi_file(fname: str) -> Tuple[Set[str], Set[str]]:
     goi = set()