wip: Add tests for data series & tags decoder

chrovis · Feb 2, 2024 · 07248bf · 07248bf
1 parent 32db818
commit 07248bf
Showing 1 changed file with 87 additions and 0 deletions.
diff --git a/test/cljam/io/cram/decode/data_series_test.clj b/test/cljam/io/cram/decode/data_series_test.clj
@@ -0,0 +1,87 @@
+(ns cljam.io.cram.decode.data-series-test
+  (:require [cljam.io.cram.decode.data-series :as ds]
+            [cljam.io.util.byte-buffer :as bb]
+            [clojure.test :refer [deftest is]]))
+
+(deftest build-data-series-decoders-test
+  (let [encodings {:BA {:codec :external, :content-id 1}
+                   :BF {:codec :external, :content-id 2}
+                   :RL {:codec :huffman, :alphabet [151], :bit-len [0]}
+                   :BB {:codec :byte-array-len
+                        :len-encoding {:codec :external, :content-id 3}
+                        :val-encoding {:codec :external, :content-id 4}}
+                   :RN {:codec :byte-array-stop, :stop-byte 0, :external-id 5}}
+        blocks [{:content-id 1
+                 :data (bb/make-lsb-byte-buffer (byte-array (.getBytes "ATGC")))}
+                {:content-id 2
+                 :data (->> (byte-array [0x80 0xa1 0x80 0x63 0x80 0xa3 0x80 0x63])
+                            bb/make-lsb-byte-buffer)}
+                {:content-id 3
+                 :data (bb/make-lsb-byte-buffer (byte-array [3 5 4 3]))}
+                {:content-id 4
+                 :data (bb/make-lsb-byte-buffer (.getBytes "CATCGAACAACTACT"))}
+                {:content-id 5
+                 :data (->> "qname001\000qname002\000qname003\000qname004\000"
+                            .getBytes
+                            bb/make-lsb-byte-buffer)}]
+        {:keys [BA BF RL BB RN]}
+        (ds/build-data-series-decoders {:data-series encodings} blocks)]
+    (is (= (map int "ATGC") [(BA) (BA) (BA) (BA)]))
+    (is (= [0xa1 0x63 0xa3 0x63] [(BF) (BF) (BF) (BF)]))
+    (is (= [151 151 151 151] [(RL) (RL) (RL) (RL)]))
+    (is (= ["CAT" "CGAAC" "AACT" "ACT"]
+           (map #(String. ^bytes %) [(BB) (BB) (BB) (BB)])))
+    (is (= ["qname001" "qname002" "qname003" "qname004"]
+           (map #(String. ^bytes %) [(RN) (RN) (RN) (RN)])))))
+
+(deftest build-tag-decoders-test
+  (let [encodings {:NM {:type \C
+                        :encoding {:codec :byte-array-len
+                                   :len-encoding {:codec :huffman
+                                                  :alphabet [1]
+                                                  :bit-len [0]}
+                                   :val-encoding {:codec :external
+                                                  :content-id 5131587}}}
+                   :pa {:type \f
+                        :encoding {:codec :byte-array-len
+                                   :len-encoding {:codec :huffman
+                                                  :alphabet [4]
+                                                  :bit-len [0]}
+                                   :val-encoding {:codec :external
+                                                  :content-id 7364966}}}
+                   :MC {:type \Z
+                        :encoding {:codec :byte-array-stop
+                                   :stop-byte 9
+                                   :external-id 5063514}}}
+        blocks [{:content-id 5131587
+                 :data (bb/make-lsb-byte-buffer (byte-array [0 1 2 0]))}
+                {:content-id 7364966
+                 :data (doto (bb/allocate-lsb-byte-buffer 16)
+                         (.putFloat 1.0)
+                         (.putFloat 0.75)
+                         (.putFloat 0.5)
+                         (.putFloat 0.0)
+                         (.flip))}
+                {:content-id 5063514
+                 :data (->> (str "151M\000\011"
+                                 "20S131M\000\011"
+                                 "16S74M1D58M2S\000\011"
+                                 "151M\000\011")
+                            .getBytes
+                            bb/make-lsb-byte-buffer)}]
+        {:keys [NM pa MC]} (ds/build-tag-decoders {:tags encodings} blocks)]
+    (is (= [{:type "i" :value 0}
+            {:type "i" :value 1}
+            {:type "i" :value 2}
+            {:type "i" :value 0}]
+           [(NM) (NM) (NM) (NM)]))
+    (is (= [{:type "f" :value 1.0}
+            {:type "f" :value 0.75}
+            {:type "f" :value 0.5}
+            {:type "f" :value 0.0}]
+           [(pa) (pa) (pa) (pa)]))
+    (is (= [{:type "Z" :value "151M"}
+            {:type "Z" :value "20S131M"}
+            {:type "Z" :value "16S74M1D58M2S"}
+            {:type "Z" :value "151M"}]
+           [(MC) (MC) (MC) (MC)]))))