Add bench code for BAM encoding

bench/cljam/io/vcf_bench.clj

@@ -1,17 +1,45 @@
 (ns cljam.io.vcf-bench
   (:require [cljam.io.vcf :as vcf]
             [cljam.test-common :as tcommon]
+            [cljam.util :as util]
+            [clojure.java.io :as cio]
             [libra.bench :refer [are defbench]]
             [libra.criterium :as c]))
 
-(defbench decode-small-bcf-bench
+(defbench encode-variant-small-bcf-bench
+  (are [f]
+       (util/with-temp-dir [d "encode-variant-small-bench"]
+         (with-open [r (vcf/reader f)
+                     w (vcf/writer (cio/file d "out.bcf")
+                                   (vcf/meta-info r)
+                                   (vcf/header r))]
+           (let [vs (vec (vcf/read-variants r))]
+             (c/quick-bench
+              (vcf/write-variants w vs)))))
+    tcommon/test-bcf-complex-file))
+
+(defbench encode-variant-large-bcf-bench
+  (tcommon/prepare-cavia!)
+  (are [f]
+       (util/with-temp-dir [d "encode-variant-large-bench"]
+         (with-open [r (vcf/reader f)
+                     w (vcf/writer (cio/file d "out.bcf")
+                                   (vcf/meta-info r)
+                                   (vcf/header r))]
+           (let [vs (vec (vcf/read-variants-randomly r {:chr "chr1" :end 30000000} {}))]
+             (c/quick-bench
+              (vcf/write-variants w vs)))))
+    tcommon/test-large-bcf-file))
+
+(defbench decode-variant-small-bcf-bench
   (are [f]
        (c/quick-bench
         (with-open [r (vcf/reader f)]
           (run! (constantly nil) (vcf/read-variants r))))
     tcommon/test-bcf-complex-file))
 
-(defbench decode-large-bcf-bench
+(defbench decode-variant-large-bcf-bench
+  (tcommon/prepare-cavia!)
   (are [f]
        (c/quick-bench
         (with-open [r (vcf/reader f)]