Add tests for rANS decoder

test-resources/cram/codecs/rans4x8/uncompressed_order1.dat

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test/cljam/io/cram/codecs/rans4x8_test.clj

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+(ns cljam.io.cram.codecs.rans4x8-test
+  (:require [cljam.io.cram.codecs.rans4x8 :as rans]
+            [cljam.io.util.byte-buffer :as bb]
+            [clojure.java.io :as io]
+            [clojure.test :refer [deftest is testing]])
+  (:import [java.io FileInputStream]
+           [java.nio ByteBuffer]
+           [java.util Arrays]))
+
+(deftest read-frequencies0-test
+  ;; cited from https://github.com/samtools/hts-specs/blob/346a94a9980b0105e926a019b4e62fa1b9e30910/CRAMcodecs.tex#L389-L394
+  (let [arr (byte-array [0x61      0x87 0x47
+                         0x62 0x02 0x82 0xe8
+                         #_>       0x81 0x74
+                         #_>       0x81 0x74
+                         0x72      0x82 0xe8
+                         0x00])
+        bb (bb/make-lsb-byte-buffer arr)]
+    (is (= {0x61 0x747
+            0x62 0x2e8
+            0x63 0x174
+            0x64 0x174
+            0x72 0x2e8}
+           (#'rans/read-frequencies0 bb)))
+    (is (zero? (.remaining bb)))))
+
+(deftest read-frequencies1-test
+  ;; cited from https://github.com/samtools/hts-specs/blob/346a94a9980b0105e926a019b4e62fa1b9e30910/CRAMcodecs.tex#L489-L516
+  (let [arr (byte-array [0x00
+                         0x61      0x8f 0xff
+                         0x00
+
+                         0x61
+                         0x61      0x82 0x86
+                         0x62 0x02 0x86 0xbd
+                         #_>       0x83 0x5e
+                         #_>       0x83 0x5e
+                         0x00
+
+                         0x62 0x02
+                         0x72      0x8f 0xff
+                         0x00
+
+                         0x61      0x8f 0xff
+                         0x00
+
+                         0x61      0x8f 0xff
+                         0x00
+
+                         0x72
+                         0x61      0x8f 0xff
+                         0x00
+
+                         0x00])
+        bb (bb/make-lsb-byte-buffer arr)]
+    (is (= {0x00 {0x61 0xfff}
+            0x61 {0x61 0x286
+                  0x62 0x6bd
+                  0x63 0x35e
+                  0x64 0x35e}
+            0x62 {0x72 0xfff}
+            0x63 {0x61 0xfff}
+            0x64 {0x61 0xfff}
+            0x72 {0x61 0xfff}}
+           (#'rans/read-frequencies1 bb)))
+    (is (zero? (.remaining bb)))))
+
+(defn- read-as-buffer ^ByteBuffer [file]
+  (with-open [in (FileInputStream. (io/file file))]
+    (let [ch (.getChannel in)
+          bb (bb/allocate-lsb-byte-buffer (.size ch))]
+      (.read ch bb)
+      (.flip bb)
+      bb)))
+
+(deftest decode-test
+  (testing "Order-0"
+    (let [uncompressed (read-as-buffer "test-resources/cram/codecs/rans4x8/uncompressed_order0.dat")
+          compressed (read-as-buffer "test-resources/cram/codecs/rans4x8/compressed_order0.dat.rans4x8")]
+      (is (Arrays/equals ^bytes (.array uncompressed) ^bytes (rans/decode compressed)))
+      (is (zero? (.remaining compressed)))))
+  (testing "Order-1"
+    (let [uncompressed (read-as-buffer "test-resources/cram/codecs/rans4x8/uncompressed_order1.dat")
+          compressed (read-as-buffer "test-resources/cram/codecs/rans4x8/compressed_order1.dat.rans4x8")]
+      (is (Arrays/equals ^bytes (.array uncompressed) ^bytes (rans/decode compressed)))
+      (is (zero? (.remaining compressed))))))