Add benchmark code for vcf-variant->protein-hgvs

Author: totakke

bench/varity/vcf_to_hgvs_bench.clj

@@ -0,0 +1,24 @@
+(ns varity.vcf-to-hgvs-bench
+  (:require [cljam.io.sequence :as cseq]
+            [libra.bench :refer :all]
+            [libra.criterium :as c]
+            [varity.ref-gene :as rg]
+            [varity.vcf-to-hgvs :as v2h]
+            [varity.t-common :refer :all]))
+
+(def variants
+  [{:chr "chr7", :pos 55191822, :ref "T", :alt "G"}
+   {:chr "chr1", :pos 247815239, :ref "AAGG", :alt "A"}
+   {:chr "chr2", :pos 26254257, :ref "G", :alt "GACT"}
+   {:chr "chr3", :pos 122740443, :ref "G", :alt "GAGA"}
+   {:chr "chr2", :pos 47445589, :ref "CTTACTGAT", :alt "CCC"}
+   {:chr "chr1", :pos 11796319, :ref "C", :alt "CGGCGGC"}
+   {:chr "chr1", :pos 69567, :ref "A", :alt "AT"}
+   {:chr "chr2", :pos 189011772, :ref "T", :alt "C"}])
+
+(defbench ^:slow vcf-variant->protein-hgvs-bench
+  (prepare-cavia!)
+  (let [rgidx (rg/index (rg/load-ref-genes test-ref-gene-file))]
+    (with-open [seq-rdr (cseq/reader test-ref-seq-file)]
+      (is (c/quick-bench (doseq [v variants]
+                           (doall (v2h/vcf-variant->protein-hgvs v seq-rdr rgidx))))))))

project.clj

@@ -25,6 +25,9 @@
   :deploy-repositories [["snapshots" {:url "https://clojars.org/repo/"
                                       :username [:env/clojars_username :gpg]
                                       :password [:env/clojars_password :gpg]}]]
+  :libra {:bench-selectors {:default (complement :slow)
+                            :slow :slow
+                            :all (constantly true)}}
   :codox {:namespaces [#"^varity\.[\w\-]+$"]
           :output-path "docs"
           :source-uri "https://github.com/chrovis/varity/blob/{version}/{filepath}#L{line}"})