Improve performance of reading BAM files.

project.clj

@@ -5,19 +5,19 @@
             :url "http://www.apache.org/licenses/LICENSE-2.0.html"}
   :dependencies [[org.clojure/tools.logging "0.3.1"]
                  [org.clojure/tools.cli "0.3.5"]
-                 [org.apache.commons/commons-compress "1.12"]
+                 [org.apache.commons/commons-compress "1.13"]
                  [me.raynes/fs "1.4.6"]
-                 [clj-sub-command "0.2.3"]
-                 [digest "1.4.4"]
+                 [clj-sub-command "0.3.0"]
+                 [digest "1.4.5"]
                  [bgzf4j "0.1.0"]
-                 [com.climate/claypoole "1.1.3"]
+                 [com.climate/claypoole "1.1.4"]
                  [camel-snake-kebab "0.4.0"]]
-  :plugins [[lein-midje "3.2"]]
+  :plugins [[lein-midje "3.2.1"]]
   :profiles {:dev {:dependencies [[org.clojure/clojure "1.8.0"]
                                   [midje "1.8.3" :exclusions [slingshot]]
-                                  [cavia "0.2.3"]]
+                                  [cavia "0.3.0"]]
                    :plugins [[lein-bin "0.3.5"]
-                             [lein-codox "0.9.5"]
+                             [lein-codox "0.10.2"]
                              [lein-marginalia "0.9.0"]]
                    :main cljam.main
                    :aot [cljam.main]

src/cljam/bam/decoder.clj

@@ -2,8 +2,7 @@
   "Decoder of BAM alignment blocks."
   (:require [clojure.string :refer [join]]
             [cljam.util :refer [ubyte hex-string->bytes]]
-            [cljam.util.sam-util :refer [phred->fastq compressed-bases->chars
-                                         ref-name]]
+            [cljam.util.sam-util :refer [phred->fastq compressed-bases->str ref-name]]
             [cljam.lsb :as lsb]
             [cljam.bam.common :refer [fixed-block-size]])
   (:import java.util.Arrays
@@ -80,7 +79,7 @@
     (phred->fastq b)))
 
 (defn decode-seq [seq-bytes length]
-  (join (compressed-bases->chars length seq-bytes 0)))
+  (compressed-bases->str length seq-bytes 0))
 
 (defn decode-next-ref-id [refs n rname]
   (cond
@@ -133,7 +132,7 @@
           qname       (lsb/read-string buffer (dec l-read-name))
           _           (lsb/skip buffer 1)
           cigar       (decode-cigar (lsb/read-bytes buffer (* n-cigar-op 4)))
-          seq         (decode-seq (lsb/read-bytes buffer (/ (inc l-seq) 2)) l-seq)
+          seq         (decode-seq (lsb/read-bytes buffer (quot (inc l-seq) 2)) l-seq)
           qual        (decode-qual (lsb/read-bytes buffer l-seq))
           rest        (lsb/read-bytes buffer (options-size (:size block)
                                                            l-read-name

src/cljam/util/sam_util.clj

@@ -2,7 +2,9 @@
   "Utilities related to SAM/BAM format."
   (:require [clojure.string :as cstr]
             [cljam.cigar :refer [count-ref]]
-            [cljam.util :refer [ubyte str->int str->float]]))
+            [cljam.util :refer [ubyte str->int str->float]])
+  (:import [java.nio CharBuffer ByteBuffer]
+           [java.nio.charset StandardCharsets]))
 
 ;;; parse
 
@@ -318,6 +320,26 @@
           (aset-byte result i (byte (bit-or h l)))
           (recur (inc i)))))))
 
+(def ^:const ^:private seq-byte-table
+  (let [nibble-table "=ACMGRSVTWYHKDBN"]
+    (->> (for [i nibble-table j nibble-table] [i j])
+         (apply concat)
+         cstr/join)))
+
+(defn compressed-bases->str
+  "Decode a sequence from byte array to String."
+  [^long length ^bytes compressed-bases ^long compressed-offset]
+  (let [cb (CharBuffer/allocate (inc length))
+        bb (ByteBuffer/wrap compressed-bases)]
+    (.position bb compressed-offset)
+    (dotimes [_ (quot (inc length) 2)]
+      (let [i (-> (.get bb) (bit-and 0xff) (* 2))]
+        (.put cb (.charAt seq-byte-table i))
+        (.put cb (.charAt seq-byte-table (inc i)))))
+    (.limit cb length)
+    (.flip cb)
+    (.toString cb)))
+
 (defn compressed-bases->chars [length compressed-bases compressed-offset]
   (let [bases (apply concat
                      (for [i (range 1 length) :when (odd? i)]
@@ -353,9 +375,16 @@
 (defmulti phred->fastq class)
 
 (defmethod phred->fastq (class (byte-array nil))
-  [b]
+  [^bytes b]
   (when-not (nil? b)
-    (cstr/join (map #(phred->fastq (int (bit-and % 0xff))) b))))
+    (let [bb (ByteBuffer/wrap b)
+          cb (CharBuffer/allocate (alength b))]
+      (loop []
+        (when (.hasRemaining bb)
+          (.put cb (char (+ 33 (.get bb))))
+          (recur)))
+      (.flip cb)
+      (.toString cb))))
 
 (def ^:const max-phred-score 93)
 

test/cljam/t_common.clj

@@ -1,6 +1,6 @@
 (ns cljam.t-common
   (:use [clojure.java.io :only [file]])
-  (:require [pandect.core :refer [md5-file]]
+  (:require [digest]
             [cljam.sam :as sam]
             [cljam.bam :as bam]
             [cljam.io :as io]
@@ -284,7 +284,7 @@
 (defn same-file?
   "Returns true if the two files' MD5 hash are same, false if not."
   [f1 f2]
-  (= (md5-file f1) (md5-file f2)))
+  (= (digest/sha1 (file f1)) (digest/sha1 (file f2))))
 
 ;;;; FASTA
 

test/cljam/util/t_sam_util.clj

@@ -3,7 +3,8 @@
   (:require [midje.sweet :refer :all]
             [cljam.t-common :refer :all]
             [cljam.util :as util]
-            [cljam.util.sam-util :as sam-util]))
+            [cljam.util.sam-util :as sam-util]
+            [clojure.string :as cstr]))
 
 (tabular
  (fact "about char->compressed-base-high"
@@ -99,6 +100,29 @@
  (util/ubyte 0xd0)   \D
  (util/ubyte 0xe0)   \B)
 
+(def nibble-table "=ACMGRSVTWYHKDBN")
+
+(tabular
+ (fact
+  "about compressed-bases->str"
+  (let [ba (byte-array (mapv util/ubyte ?bases))]
+    (cstr/join (sam-util/compressed-bases->chars ?length ba ?offset)) => ?expected
+    (sam-util/compressed-bases->str ?length ba ?offset) => ?expected))
+ ?length  ?bases                                    ?offset  ?expected
+ 1        [0x00]                                    0        "="
+ 2        [0x00]                                    0        "=="
+ 1        [0x10]                                    0        "A"
+ 2        [0x12]                                    0        "AC"
+ 4        [0x12 0x8F]                               0        "ACTN"
+ 1        [0x12 0x8F]                               1        "T"
+ 2        [0x12 0x8F]                               1        "TN"
+ 16       [0x01 0x23 0x45 0x67 0x89 0xAB 0xCD 0xEF] 0        nibble-table
+ 14       [0x01 0x23 0x45 0x67 0x89 0xAB 0xCD 0xEF] 1        (subs nibble-table 2)
+ 2        [0x01 0x23 0x45 0x67 0x89 0xAB 0xCD 0xEF] 7        "BN"
+ 512      (range 256)                               0        (->> (for [i nibble-table j nibble-table] [i j])
+                                                                  (apply concat)
+                                                                  cstr/join))
+
 ;; Reference functions
 ;; -------------------