Add codec benchmark

bench/cljam/io/bam/decoder_bench.clj

@@ -0,0 +1,21 @@
+(ns cljam.io.bam.decoder-bench
+  (:require [libra.bench :refer [defbench are]]
+            [libra.criterium :as c]
+            [cljam.test-common :as tcommon]
+            [cljam.io.sam :as sam]))
+
+(defbench decode-bam-alignment-short-bench
+  (are [f]
+       (c/quick-bench
+        (with-open [r (sam/reader f)]
+          (dorun (sam/read-alignments r))))
+    tcommon/test-bam-file
+    tcommon/medium-bam-file
+    tcommon/codec-benchmark-bam-file))
+
+(defbench decode-bam-alignment-long-bench
+  (are [f]
+       (c/quick-bench
+        (with-open [r (sam/reader f)]
+          (dorun (vec (take 10000000 (sam/read-alignments r))))))
+    tcommon/large-bam-file))

bench/cljam/io/bam/encoder_bench.clj

@@ -0,0 +1,31 @@
+(ns cljam.io.bam.encoder-bench
+  (:require [libra.bench :refer [defbench are]]
+            [libra.criterium :as c]
+            [cljam.test-common :as tcommon]
+            [cljam.io.sam :as sam]))
+
+(defbench encode-alignment-short-bench
+  (tcommon/with-before-after {:before (tcommon/prepare-cache!)
+                              :after (tcommon/clean-cache!)}
+    (are [f]
+         (with-open
+          [r (sam/reader f)
+           w (sam/writer (str tcommon/temp-dir "/encode-alignment-bench.bam"))]
+           (let [header (sam/read-header r)
+                 aln (sam/read-alignments r)]
+             (c/quick-bench (sam/write-alignments w aln header))))
+      tcommon/test-sam-file
+      tcommon/medium-sam-file
+      tcommon/codec-benchmark-sam-file)))
+
+(defbench encode-alignment-long-bench
+  (tcommon/with-before-after {:before (tcommon/prepare-cache!)
+                              :after (tcommon/clean-cache!)}
+    (are [f]
+         (with-open
+          [r (sam/reader f)
+           w (sam/writer (str tcommon/temp-dir "/encode-alignment-bench.bam"))]
+           (let [header (sam/read-header r)
+                 aln (sam/read-alignments r)]
+             (c/quick-bench (sam/write-alignments w (vec (take 2000000 aln)) header))))
+      tcommon/large-bam-file)))