variant.best_vep()

src/variant/variant_collection.rs

@@ -19,8 +19,8 @@ use crate::{
     annotation::{
         cosmic::Cosmic,
         echtvar::{parse_echtvar_val, run_echtvar},
-        gnomad::{GnomAD, GnomADValue},
-        vep::{run_vep, VepLine, VEP},
+        gnomad::GnomAD,
+        vep::{get_best_vep, run_vep, VepLine, VEP},
         Annotation, Annotations,
     },
     collection::{
@@ -30,7 +30,6 @@ use crate::{
     helpers::{app_storage_dir, estimate_shannon_entropy, mean, temp_file_path, Hash128},
     io::{fasta::sequence_at, readers::get_reader, vcf::vcf_header},
     positions::GenomePosition,
-    variant::variant::Format,
 };
 
 /// A collection of VCF variants along with associated metadata.
@@ -437,6 +436,10 @@ impl Variant {
             .collect()
     }
 
+    pub fn best_vep(&self) -> anyhow::Result<VEP> {
+        get_best_vep(&self.vep())
+    }
+
     pub fn alteration_category(&self) -> Vec<AlterationCategory> {
         self.vcf_variants
             .iter()