Merge pull request #189 from chrovis/spike/cache-replacement-for-cigar

Replace memoizing cache for parsed CIGARs with core.memoize's LU cache

project.clj

@@ -3,7 +3,8 @@
   :url "https://github.com/chrovis/cljam"
   :license {:name "Apache License, Version 2.0"
             :url "https://www.apache.org/licenses/LICENSE-2.0"}
-  :dependencies [[org.clojure/tools.logging "0.5.0"]
+  :dependencies [[org.clojure/core.memoize "0.8.2"]
+                 [org.clojure/tools.logging "0.5.0"]
                  [org.clojure/tools.cli "0.4.2"]
                  [org.apache.commons/commons-compress "1.19"]
                  [clj-sub-command "0.5.1"]

src/cljam/io/sam/util/cigar.clj

@@ -1,5 +1,7 @@
 (ns cljam.io.sam.util.cigar
   "Parser of CIGAR strings."
+  (:require [clojure.core.memoize :as memoize]
+            [proton.core :as proton])
   (:import [java.nio ByteBuffer ByteOrder]))
 
 (defn parse
@@ -45,7 +47,10 @@
           #{\I} (recur xs r (+ s l) (update-last! idx (fn [x] [:i x [s (+ l s)]]))))
         (persistent! idx)))))
 
-(def to-index (memoize to-index*))
+(def to-index
+  (memoize/lu to-index* :lu/threshold
+              (or (proton/as-int (System/getProperty "cljam.sam.cigar.cache-size"))
+                  1024)))
 
 (defn count-op
   "Returns length of CIGAR operations."