Filter invalid alleles

Author: bpblanken

v03_pipeline/lib/reference_datasets/hmtvar.py

@@ -1,6 +1,7 @@
 import hail as hl
 import requests
 
+from v03_pipeline.lib.model.dataset_type import DatasetType
 from v03_pipeline.lib.model.definitions import ReferenceGenome
 
 
@@ -21,4 +22,9 @@ def get_ht(
         score=ht.disease_score,
     )
     ht = ht.key_by('locus', 'alleles')
+    ht = ht.filter(
+        ~DatasetType.SNV_INDEL.invalid_allele_types.contains(
+            hl.numeric_allele_type(ht.alleles[0], ht.alleles[1]),
+        ),
+    )
     return ht.group_by(*ht.key).aggregate(score=hl.agg.max(ht.score))