Fix broken tests

chrovis · Nov 22, 2023 · 37c18ed · 37c18ed
1 parent 8961c28
commit 37c18ed
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Showing 3 changed files with 25 additions and 32 deletions.
diff --git a/test/cljam/io/bam/encoder_test.clj b/test/cljam/io/bam/encoder_test.clj
@@ -4,13 +4,12 @@
             [clojure.string :as cstr]
             [cljam.io.bam.encoder :as encoder]
             [cljam.test-common :as test-common])
-  (:import [java.io ByteArrayOutputStream DataOutputStream]
-           [java.nio ByteBuffer ByteOrder]))
+  (:import [java.io ByteArrayOutputStream DataOutputStream]))
 
 (defn- get-encoded-option-data [?type ?values]
-  (let [bb (ByteBuffer/allocate 200)]
-    (#'encoder/encode-tag-value bb ?type ?values)
-    (take (.position bb) (.array bb))))
+  (let [baos (ByteArrayOutputStream.)]
+    (#'encoder/encode-tag-value baos ?type ?values)
+    (seq (.toByteArray baos))))
 
 (deftest encode-tag-value-test
   (testing "non-array types"
@@ -175,12 +174,11 @@
               ))]
 
     (are [?aln ?expected-byte]
-         (= (doto (ByteBuffer/wrap (byte-array (map unchecked-byte ?expected-byte)))
-              (.order ByteOrder/LITTLE_ENDIAN))
-            (with-open [baos (ByteArrayOutputStream. 4096)
+         (= ?expected-byte
+            (with-open [baos (ByteArrayOutputStream.)
                         dos (DataOutputStream. baos)]
               (encoder/encode-alignment dos ?aln '({:name "ref", :len 0}))
-              (ByteBuffer/wrap (byte-array (.toByteArray baos)))))
+              (seq (.toByteArray baos))))
 
       (test-common/to-sam-alignment
        {:qname "r003", :flag 16, :rname "ref", :pos 29, :end 33, :mapq 30,

diff --git a/test/cljam/io/bam_test.clj b/test/cljam/io/bam_test.clj
@@ -1,18 +1,18 @@
 (ns cljam.io.bam-test
   "Tests for Processing BAM files."
-  (:require [clojure.test :refer [deftest are testing]]
+  (:require [cljam.io.bam.decoder :as decoder]
             [cljam.io.bam.encoder :as encoder]
-            [cljam.io.bam.decoder :as decoder])
-  (:import [java.nio ByteBuffer]))
+            [cljam.io.util.byte-buffer :as bb]
+            [clojure.test :refer [are deftest testing]])
+  (:import [java.io ByteArrayOutputStream]))
 
 (deftest aux-data-codec-test
   (testing "non-array types"
     (are [?type ?value]
          (= ?value
-            (as-> (#'encoder/encode-tag-value
-                   (ByteBuffer/allocate 100) ?type ?value) ^ByteBuffer bb
-              (.position bb 0)
-              (decoder/parse-tag-single ?type bb)))
+            (let [baos (ByteArrayOutputStream.)]
+              (#'encoder/encode-tag-value baos ?type ?value)
+              (decoder/parse-tag-single ?type (bb/make-lsb-byte-buffer (.toByteArray baos)))))
       \A \@
       \A \A
       \A \z
@@ -52,22 +52,19 @@
   (testing "NULL-terminated text"
     (are [?type ?value]
          (= ?value
-            (as-> (#'encoder/encode-tag-value
-                   (ByteBuffer/allocate 100) ?type ?value) ^ByteBuffer bb
-              (.position bb 0)
-              (decoder/parse-tag-single ?type bb)))
+            (let [baos (ByteArrayOutputStream.)]
+              (#'encoder/encode-tag-value baos ?type ?value)
+              (decoder/parse-tag-single ?type (bb/make-lsb-byte-buffer (.toByteArray baos)))))
       \Z "aaaBBB0011223344@@@+++"
       \Z (str "!\"#$%&'()*+,-./0123456789:;<=>?@"
               "ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz{|}~")))
 
   (testing "array types"
     (are [?value]
          (= ?value
-            (as->
-             (#'encoder/encode-tag-value
-              (ByteBuffer/allocate 100) \B ?value) ^ByteBuffer bb
-              (.position bb 0)
-              (#'decoder/parse-tag-array bb)))
+            (let [baos (ByteArrayOutputStream.)]
+              (#'encoder/encode-tag-value baos \B ?value)
+              (#'decoder/parse-tag-array (bb/make-lsb-byte-buffer (.toByteArray baos)))))
       "c,0"
       "C,0"
       "s,0"

diff --git a/test/cljam/io/bcf/reader_test.clj b/test/cljam/io/bcf/reader_test.clj
@@ -1,17 +1,15 @@
 (ns cljam.io.bcf.reader-test
-  (:require [clojure.test :refer [deftest are]]
-            [cljam.io.bcf.reader :as bcf-reader])
-  (:import [java.nio ByteBuffer ByteOrder]))
+  (:require [cljam.io.bcf.reader :as bcf-reader]
+            [clojure.test :refer [are deftest]])
+  (:import [java.io ByteArrayInputStream]))
 
 (deftest parse-data-line-deep
   (are [?bytes ?var]
        (= ?var
           (@#'bcf-reader/parse-data-line-deep
            (@#'bcf-reader/read-data-line-buffer
-            (doto (ByteBuffer/wrap
-                   (byte-array
-                    (map unchecked-byte ?bytes)))
-              (.order ByteOrder/LITTLE_ENDIAN)))))
+            (ByteArrayInputStream.
+             (byte-array (map unchecked-byte ?bytes))))))
     [0x1c 0x00 0x00 0x00
      0x00 0x00 0x00 0x00
      0x00 0x00 0x00 0x00