issue SACGF/variantgrid_private#3676 - correctly calculate Variant.end

snpdb/management/commands/one_off_fix_variant_end.py

@@ -4,7 +4,7 @@
 from django.conf import settings
 from django.core.management.base import BaseCommand
 from django.db.models import OuterRef, Subquery, F
-from django.db.models.functions import Length
+from django.db.models.functions import Length, Abs
 
 from annotation.models import AnnotationRangeLock
 from library.utils import mk_path
@@ -28,10 +28,15 @@ def add_arguments(self, parser):
     @staticmethod
     def update_variants_in_range_fix_end(variant_qs):
         # These are all non-symbolic, so can just use ref length
-        variant_qs = variant_qs.exclude(alt__seq__startswith="<")
-        calc_end = F("locus__position") + Length("locus__ref__seq")
-        variant_subquery = Variant.objects.filter(pk=OuterRef("pk")).annotate(calc_end=calc_end).values("calc_end")[:1]
-        variant_qs.update(end=Subquery(variant_subquery))
+        non_symbolic_variant_qs = variant_qs.filter(svlen__isnull=True)
+        calc_end = F("locus__position") + Length("locus__ref__seq") - 1
+        non_symbolic_variant_subquery = Variant.objects.filter(pk=OuterRef("pk")).annotate(calc_end=calc_end).values("calc_end")[:1]
+        non_symbolic_variant_qs.update(end=Subquery(non_symbolic_variant_subquery))
+
+        symbolic_variant_qs = variant_qs.filter(svlen__isnull=False)
+        calc_end = F("locus__position") + Abs("svlen")
+        symbolic_variant_subquery = Variant.objects.filter(pk=OuterRef("pk")).annotate(calc_end=calc_end).values("calc_end")[:1]
+        symbolic_variant_qs.update(end=Subquery(symbolic_variant_subquery))
 
     def handle(self, *args, **options):
         # We want to do this in small batches - so use the variant annotation range locks which are all approx the same
@@ -43,7 +48,7 @@ def handle(self, *args, **options):
         # This can take a few days, so we'll write the variant as we go, so we can resume without any troubles
         migrations_dir = os.path.join(settings.PRIVATE_DATA_ROOT, "migrations")
         mk_path(migrations_dir)
-        progress_file = os.path.join(migrations_dir, "one_off_fix_variant_end_progress.txt")
+        progress_file = os.path.join(migrations_dir, "one_off_fix_variant_end_progress_v2.txt")
 
         highest_av = AnnotationRangeLock.objects.order_by("-max_variant").first()
         arl_qs = AnnotationRangeLock.objects.filter(version=highest_av.version)

snpdb/models/models_variant.py

@@ -252,11 +252,9 @@ def end(self) -> int:
                 * <DEL>, <DUP>, <INV>, and <CNV> symbolic structural variant alleles:, POS + SVLEN
         """
         if self.is_symbolic():
-            # Insertions add w/o replacing, so their end is the start (ie 1 past start using half-open)
-            if self.alt == VCFSymbolicAllele.DUP:
-                return self.position + 1
-            return self.position + abs(self.svlen) + 1
-        return self.position + len(self.ref)
+            # We don't support <INV> so don't need to worry about it
+            return self.position + abs(self.svlen)
+        return self.position + len(self.ref) - 1
 
     def __lt__(self, other):
         return self.as_tuple < other.as_tuple