fixed TODO Strings Returned as Real Variant Effect Values

Author: blankirigaya

malariagen_data/veff.py

@@ -539,7 +539,11 @@ def _get_within_intron_effect(base_effect, intron):
             effect = base_effect._replace(effect="INTRONIC", impact="MODIFIER")
 
     else:
-        # TODO intronic INDELs and MNPs
-        effect = base_effect._replace(effect="TODO intronic indels and MNPs")
+        if intron_min_dist <= 2:
+            effect = base_effect._replace(effect="SPLICE_CORE", impact="HIGH")
+        elif intron_min_dist <= 7:
+            effect = base_effect._replace(effect="SPLICE_REGION", impact="MODERATE")
+        else:
+            effect = base_effect._replace(effect="INTRONIC", impact="MODIFIER")
 
     return effect