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wip: Add test for structures
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@athos
athos committed Feb 9, 2024
1 parent c86f8f9 commit e1d5769
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Binary file added test-resources/cram/medium_with_standard_tags.cram
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164 changes: 164 additions & 0 deletions test/cljam/io/cram/decode/structure_test.clj
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(ns cljam.io.cram.decode.structure-test
(:require [cljam.io.cram.decode.structure :as struct]
[cljam.io.sam :as sam]
[cljam.io.util.byte-buffer :as bb]
[cljam.test-common :as common]
[clojure.java.io :as cio]
[clojure.test :refer [deftest is]])
(:import [java.io FileInputStream]
[java.nio ByteOrder]
[java.nio.channels FileChannel$MapMode]))

(defn- bytes->vec [bs]
(mapv #(bit-and (long %) 0xff) bs))

(defn- decode-container-header [bb]
(-> (struct/decode-container-header bb)
(update :landmarks bytes->vec)
(update :crc bytes->vec)))

(deftest cram-file-structure-decode-test
(with-open [fis (FileInputStream. (cio/file common/medium-with-standard-tags-cram-file))
ch (.getChannel fis)]
(let [bb (-> ch
(.map FileChannel$MapMode/READ_ONLY 0 (.size ch))
(.order ByteOrder/LITTLE_ENDIAN))]
(is (= {:version {:major 3 :minor 0}
:id "file:///tmp/cljam/me"}
(struct/decode-file-definition bb)))
(is (= {:length 278
:ref -1
:start 0
:span 0
:records 0
:counter 0
:bases 0
:blocks 1
:landmarks []
:crc [240 201 140 91]}
(decode-container-header bb)))
(is (= (with-open [r (sam/reader common/medium-bam-file)]
(merge {:HD {:VN "1.6" :SO "unsorted"}}
(sam/read-header r)))
(struct/decode-cram-header-block bb)))
(is (= {:length 362828
:ref -2
:start 0
:span 0
:records 10000
:counter 0
:bases 760000
:blocks 29
:landmarks [207]
:crc [246 184 214 91]}
(decode-container-header bb)))
(is (= {:preservation-map
{:RN true
:AP false
:RR true
:SM
{\A {0 \G, 1 \C, 2 \T, 3 \N}
\C {0 \G, 1 \T, 2 \A, 3 \N}
\G {0 \A, 1 \C, 2 \T, 3 \N}
\T {0 \C, 1 \G, 2 \A, 3 \N}
\N {0 \A, 1 \C, 2 \G, 3 \T}}
:TD [[]
[{:tag :MD, :type \Z} {:tag :NM, :type \c}]]}
:data-series
{:BF {:codec :external, :content-id 1}
:CF {:codec :external, :content-id 2}
:RI {:codec :external, :content-id 3}
:RL {:codec :external, :content-id 4}
:AP {:codec :external, :content-id 5}
:RG {:codec :external, :content-id 6}
:RN {:codec :byte-array-stop, :stop-byte 9, :external-id 7}
:NF {:codec :external, :content-id 8}
:MF {:codec :external, :content-id 9}
:NS {:codec :external, :content-id 10}
:NP {:codec :external, :content-id 11}
:TS {:codec :external, :content-id 12}
:TL {:codec :external, :content-id 13}
:MQ {:codec :external, :content-id 16}
:FN {:codec :external, :content-id 17}
:FP {:codec :external, :content-id 18}
:FC {:codec :external, :content-id 19}
:BA {:codec :external, :content-id 22}
:QS {:codec :external, :content-id 23}
:BS {:codec :external, :content-id 24}
:IN {:codec :byte-array-stop, :stop-byte 9, :external-id 25}
:DL {:codec :external, :content-id 26}
:RS {:codec :external, :content-id 27}
:SC {:codec :byte-array-stop, :stop-byte 9, :external-id 28}
:PD {:codec :external, :content-id 29}
:HC {:codec :external, :content-id 30}}
:tags
{:MD
{\Z {:codec :byte-array-stop, :stop-byte 9, :external-id 5063770}}
:NM
{\c
{:codec :byte-array-len
:len-encoding {:codec :huffman, :alphabet [1], :bit-len [0]}
:val-encoding {:codec :external, :content-id 5131619}}}}}
(struct/decode-compression-header-block bb)))
(is (= {:tags []
:content-ids
[1 2 3 4 5 6 7 8 9 10 11 12 13 16 17 18 19
22 23 24 25 26 27 28 29 30 5063770 5131619]
:start 0
:reference-md5 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
:records 10000
:counter 0
:blocks 29
:embedded-reference -1
:ref-seq-id -2
:span 0}
(-> (struct/decode-slice-header-block bb)
(update :reference-md5 bytes->vec))))
(is (= [{:method 0, :content-type 5, :content-id 0, :size 0, :raw-size 0, :crc [47 7 252 241]}
{:method 4, :content-type 4, :content-id 1, :size 1039, :raw-size 10000, :crc [202 95 54 132]}
{:method 4, :content-type 4, :content-id 2, :size 36, :raw-size 10000, :crc [87 22 235 242]}
{:method 4, :content-type 4, :content-id 3, :size 6684, :raw-size 18308, :crc [1 15 226 78]}
{:method 4, :content-type 4, :content-id 4, :size 36, :raw-size 10000, :crc [166 191 130 64]}
{:method 4, :content-type 4, :content-id 5, :size 31125, :raw-size 33411, :crc [179 8 47 242]}
{:method 4, :content-type 4, :content-id 6, :size 36, :raw-size 50000, :crc [249 83 125 26]}
{:method 1, :content-type 4, :content-id 7, :size 77500, :raw-size 411343, :crc [1 19 161 227]}
{:method 1, :content-type 4, :content-id 8, :size 20, :raw-size 0, :crc [100 132 79 154]}
{:method 1, :content-type 4, :content-id 9, :size 45, :raw-size 10000, :crc [90 129 139 84]}
{:method 4, :content-type 4, :content-id 10, :size 36, :raw-size 50000, :crc [243 129 185 33]}
{:method 1, :content-type 4, :content-id 11, :size 45, :raw-size 10000, :crc [61 217 74 145]}
{:method 4, :content-type 4, :content-id 12, :size 31, :raw-size 10000, :crc [46 244 148 239]}
{:method 1, :content-type 4, :content-id 13, :size 48, :raw-size 10000, :crc [239 168 203 254]}
{:method 1, :content-type 4, :content-id 16, :size 1977, :raw-size 7923, :crc [248 27 134 197]}
{:method 1, :content-type 4, :content-id 17, :size 2046, :raw-size 7923, :crc [61 142 4 22]}
{:method 1, :content-type 4, :content-id 18, :size 3458, :raw-size 4616, :crc [61 182 157 145]}
{:method 1, :content-type 4, :content-id 19, :size 271, :raw-size 4616, :crc [88 186 74 54]}
{:method 4, :content-type 4, :content-id 22, :size 37161, :raw-size 157901, :crc [226 220 219 56]}
{:method 4, :content-type 4, :content-id 23, :size 187340, :raw-size 760000, :crc [227 117 208 184]}
{:method 1, :content-type 4, :content-id 24, :size 1377, :raw-size 4493, :crc [28 234 48 60]}
{:method 1, :content-type 4, :content-id 25, :size 20, :raw-size 0, :crc [252 232 78 0]}
{:method 1, :content-type 4, :content-id 26, :size 47, :raw-size 73, :crc [87 78 224 195]}
{:method 1, :content-type 4, :content-id 27, :size 20, :raw-size 0, :crc [21 59 216 237]}
{:method 1, :content-type 4, :content-id 28, :size 23, :raw-size 3, :crc [186 219 248 202]}
{:method 1, :content-type 4, :content-id 29, :size 20, :raw-size 0, :crc [111 73 18 0]}
{:method 1, :content-type 4, :content-id 30, :size 20, :raw-size 0, :crc [82 112 247 118]}
{:method 4, :content-type 4, :content-id 5063770, :size 10053, :raw-size 43243, :crc [246 219 153 220]}
{:method 4, :content-type 4, :content-id 5131619, :size 1492, :raw-size 7923, :crc [161 9 102 22]}]
(mapv (fn [_]
(-> (struct/decode-block bb)
(update :crc bytes->vec)
(dissoc :data)))
(range 29))))
(let [container-header (decode-container-header bb)]
(is (= {:length 98171
:ref -1
:start 0
:span 0
:records 2271
:counter 10000
:bases 172596
:blocks 29
:landmarks [171]
:crc [228 46 96 120]}
container-header))
(bb/skip bb (:length container-header))
(is (struct/eof-container? (decode-container-header bb)))))))
4 changes: 4 additions & 0 deletions test/cljam/test_common.clj
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Expand Up @@ -160,6 +160,10 @@
(def test-bai-file "test-resources/bam/test.sorted.bam.bai")
(def test-large-bai-file (cavia/resource mycavia "large.bai"))

;; ### CRAM file

(def medium-with-standard-tags-cram-file "test-resources/cram/medium_with_standard_tags.cram")

;; ### FASTA files

(def test-fa-file "test-resources/fasta/test.fa")
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