bam_test.clj

(ns cljam.io.bam-test
  "Tests for Processing BAM files."
  (:require [clojure.test :refer [deftest are testing]]
            [cljam.io.bam.encoder :as encoder]
            [cljam.io.bam.decoder :as decoder])
  (:import [java.nio ByteBuffer]))

(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) ?type ?value))
      \A \@
      \A \A
      \A \z
      \c -128
      \c -1
      \c 0
      \c 127
      \C 0
      \C 127
      \C 128
      \C 255
      \s -32768
      \s -1
      \s 0
      \s 32767
      \S 0
      \S 32767
      \S 32768
      \S 65535
      \i -2147483648
      \i 0
      \i -1
      \i 2147483647
      \I 0
      \I 2147483647
      \I 2147483648
      \I 4294967295
      \f -17.75
      \f 0.0
      \f 5.75
      \f (Float/MAX_VALUE)
      \f (Float/MIN_NORMAL)
      \f (Float/MIN_VALUE)
      \f (Float/NEGATIVE_INFINITY)
      \f (Float/POSITIVE_INFINITY)))

  (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) ?type ?value))
      \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)))
      "c,0"
      "C,0"
      "s,0"
      "S,0"
      "i,0"
      "I,0"
      "f,0.0"
      "c,-128,0,127"
      "C,0,255"
      "s,-32768,0,32767"
      "S,0,65535"
      "i,-2147483648,0,2147483647"
      "I,0,4294967295"
      "f,-17.25,0.0,5.75"
      "f,3.4028235E38,1.17549435E-38,1.4E-45,-Infinity,Infinity")))