Merge pull request #63 from ayamada/feature/test-check-deduped-file

Issue #61 (6) Examine result file of `dedupe` in test

test/cljam/t_common.clj

@@ -107,6 +107,9 @@
 (def medium-bam-file "test-resources/medium.bam")
 (def large-bam-file (cavia/resource mycavia "large.bam"))
 
+(def dedupe-before-bam-file "test-resources/dedupe_before.bam")
+(def dedupe-after-bam-file "test-resources/dedupe_after.bam")
+
 ;; ### BAM index files
 
 (def test-bai-file "test-resources/test.sorted.bam.bai")
@@ -377,6 +380,15 @@
   [f1 f2]
   (= (digest/sha1 (file f1)) (digest/sha1 (file f2))))
 
+(defn same-bam-file?
+  [f1 f2]
+  (with-open [r1 (bam/reader f1)
+              r2 (bam/reader f2)]
+    (and (= (io/read-header r1)
+            (io/read-header r2))
+         (= (io/read-alignments r1 {})
+            (io/read-alignments r2 {})))))
+
 ;;;; FASTA
 
 (def test-fa-header [{:desc "", :name "ref", :offset 5} {:desc "", :name "ref2", :offset 57}])

test/cljam/t_dedupe.clj

@@ -8,12 +8,9 @@
 (deftest simple-pe-dedupe
   (with-before-after {:before (prepare-cache!)
                       :after (clean-cache!)}
-    ;; TODO: need bam-file include PCR duplications
-    (let [in-file test-sorted-bam-file
-          out-file (str temp-dir "/deduped.bam")]
-      (is (not-throw? (dedupe/dedupe in-file out-file)))
-      ;; TODO: check alignments of out-file
-      )))
+    (let [out-file (str temp-dir "/deduped.bam")]
+      (is (not-throw? (dedupe/dedupe dedupe-before-bam-file out-file)))
+      (is (same-bam-file? out-file dedupe-after-bam-file)))))
 
 (deftest simple-pe-dedupe-xform
   (is (= (into #{}