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chrovis · Feb 6, 2024 · 4eadd5b · 4eadd5b
1 parent 7228150
commit 4eadd5b
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Showing 3 changed files with 35 additions and 38 deletions.
diff --git a/src/cljam/io/cram/decode/data_series.clj b/src/cljam/io/cram/decode/data_series.clj
@@ -1,7 +1,8 @@
 (ns cljam.io.cram.decode.data-series
   {:clj-kondo/ignore [:missing-docstring]}
   (:require [cljam.io.cram.itf8 :as itf8]
-            [cljam.io.util.byte-buffer :as bb])
+            [cljam.io.util.byte-buffer :as bb]
+            [clojure.string :as str])
   (:import [java.nio Buffer ByteBuffer]))
 
 (defn- data-series-type [ds]
@@ -48,8 +49,11 @@
       (fn []
         (.mark ^Buffer block)
         (let [start (.position block)
-              end (do (while (not= (.get block) (byte stop-byte)))
-                      (.position block))
+              end (long
+                   (loop []
+                     (if (= (.get block) (byte stop-byte))
+                       (.position block)
+                       (recur))))
               len (dec (- end start))
               _ (.reset ^Buffer block)
               ret (bb/read-bytes block len)]
@@ -84,26 +88,11 @@
                (aset arr i (byte b))))
            arr))
     \B (fn [^ByteBuffer bb]
-         (let [tag-type' (.get bb)
+         (let [tag-type' (char (.get bb))
                len (.getInt bb)
-               coercer (tag-value-coercer tag-type')]
-           (case (char tag-type')
-             (\c \C) (let [arr (byte-array len)]
-                       (dotimes [i len]
-                         (aset arr i (byte (coercer bb))))
-                       arr)
-             (\s \S) (let [arr (short-array len)]
-                       (dotimes [i len]
-                         (aset arr i (short (coercer bb))))
-                       arr)
-             (\i \I) (let [arr (int-array len)]
-                       (dotimes [i len]
-                         (aset arr i (int (coercer bb))))
-                       arr)
-             (\f) (let [arr (float-array len)]
-                    (dotimes [i len]
-                      (aset arr i (float (coercer bb))))
-                    arr))))))
+               coercer (tag-value-coercer tag-type')
+               vs (repeatedly len (partial coercer bb))]
+           (str/join \, (cons tag-type' vs))))))
 
 (defn- build-tag-decoder [tag-encoding tag-type content-id->block-data]
   (let [decoder (build-codec-decoder tag-encoding :bytes content-id->block-data)
@@ -114,8 +103,13 @@
 
 (defn build-tag-decoders [{:keys [tags]} blocks]
   (let [content-id->block-data (into {} (map (juxt :content-id :data)) blocks)]
-    (reduce-kv (fn [decoders tag {tag-type :type :keys [encoding]}]
-                 (let [decoder (build-tag-decoder encoding tag-type content-id->block-data)
-                       tag-type' (str (if (#{\c \C \s \S \i \I} tag-type) \i tag-type))]
-                   (assoc decoders tag (fn [] {:type tag-type' :value (decoder)}))))
-               {} tags)))
+    (reduce-kv
+     (fn [decoders tag m]
+       (reduce-kv
+        (fn [decoders tag-type encoding]
+          (let [decoder (build-tag-decoder encoding tag-type content-id->block-data)
+                tag-type' (str (if (#{\c \C \s \S \i \I} tag-type) \i tag-type))]
+            (assoc-in decoders [tag tag-type]
+                      (fn [] {:type tag-type' :value (decoder)}))))
+        decoders m))
+     {} tags)))
diff --git a/src/cljam/io/cram/decode/record.clj b/src/cljam/io/cram/decode/record.clj
@@ -51,16 +51,19 @@
           (assoc ::next-fragment (NF)))))))
 
 (defn- build-auxiliary-tags-decoder [{:keys [preservation-map]} {:keys [TL]} tag-decoders]
-  (let [tag-dict (:TD preservation-map)]
+  (let [tag-decoder (fn [{tag-type :type :keys [tag]}]
+                      (let [decoder (get-in tag-decoders [tag tag-type])]
+                        (fn []
+                          {tag (decoder)})))
+        decoders (mapv (fn [tags]
+                         (let [decoders (mapv tag-decoder tags)]
+                           (fn []
+                             (into [] (map #(%)) decoders))))
+                       (:TD preservation-map))]
     (fn [record]
       (let [tl (TL)
-            tags (nth tag-dict tl)]
-        (->> tags
-             (reduce (fn [acc {:keys [tag]}]
-                       (let [decoder (get tag-decoders tag)]
-                         (conj acc {tag (decoder)})))
-                     [])
-             (assoc record :options))))))
+            decoder (nth decoders tl)]
+        (assoc record :options (decoder))))))
 
 (defn- record-seq
   [seq-resolver {:keys [preservation-map]} {:keys [rname pos end] :as record} features]

diff --git a/src/cljam/io/cram/decode/structure.clj b/src/cljam/io/cram/decode/structure.clj
@@ -173,16 +173,16 @@
 (defn- decode-tag-encoding-map [bb]
   (let [_size (itf8/decode-itf8 bb)
         n (itf8/decode-itf8 bb)]
-    (loop [i n, acc (transient {})]
+    (loop [i n, acc {}]
       (if (zero? i)
-        (persistent! acc)
+        acc
         (let [k (itf8/decode-itf8 bb)
               c1 (char (bit-and (bit-shift-right k 16) 0xff))
               c2 (char (bit-and (bit-shift-right k 8) 0xff))
               t (char (bit-and k 0xff))
               v (decode-encoding bb)
               tag (keyword (str c1 c2))]
-          (recur (dec i) (assoc! acc tag {:type t :encoding v})))))))
+          (recur (dec i) (assoc-in acc [tag t] v)))))))
 
 (defn decode-compression-header-block [bb]
   (let [{bb' :data} (decode-block bb)