test: Add bench.

Author: niyarin

bench/varity/large_vcf_lift_bench.clj

@@ -0,0 +1,17 @@
+(ns varity.large-vcf-lift-bench
+  (:require [libra.bench :refer :all]
+            [libra.criterium :as c]
+            [cljam.io.sequence :as cseq]
+            [cljam.io.vcf :as vcf]
+            [varity.chain :as ch]
+            [varity.vcf-lift :as vcf-lift]
+            [varity.t-common :refer :all]))
+
+(defbench large-vcf-lift-bench
+  (prepare-cavia!)
+  (with-open [seq-rdr (cseq/reader test-ref-seq-file)
+              vcf-rdr (vcf/reader test-large-vcf-file)]
+    (let [chidx (ch/index (ch/load-chain test-large-chain-file))]
+      (is (c/quick-bench
+           (doall (vcf-lift/liftover-variants
+                   seq-rdr chidx (vcf/read-variants vcf-rdr))))))))

test-resources/large.chain.gz

@@ -73,3 +73,9 @@
 (def test-load-refgene-file "./test-resources/test-refgene.txt")
 
 (def test-load-refseq-file "./test-resources/test-refseq.txt")
+
+(def test-gtf-file "./test-resources/gtf_parse_test.gtf")
+
+(def test-large-chain-file "./test-resources/large.chain.gz")
+
+(def test-large-vcf-file "./test-resources/large.vcf.gz")