Add ancestral allele

tskit-dev · Oct 31, 2022 · 01af015 · 01af015
1 parent 9927560
commit 01af015
Showing 1 changed file with 9 additions and 0 deletions.
diff --git a/tsinfer/formats.py b/tsinfer/formats.py
@@ -2289,6 +2289,15 @@ def sites_position(self):
     def sites_alleles(self):
         return self.data["variant_allele"]
 
+    @property
+    def sites_ancestral_allele(self):
+        try:
+            return self.data["sites/ancestral_allele"]
+        except KeyError:
+            # Maintains backwards compatibility: in previous tsinfer versions the
+            # ancestral allele was always the zeroth element in the alleles list
+            return np.zeros(self.num_sites, dtype=np.int8)
+
     @property
     def sites_genotypes(self):
         gt = self.data["call_genotype"]