Add tests for cram reader

test/cljam/io/cram_test.clj

@@ -0,0 +1,40 @@
+(ns cljam.io.cram-test
+  (:require [cljam.io.cram :as cram]
+            [cljam.io.sam :as sam]
+            [cljam.test-common :as common :refer [deftest-remote
+                                                  prepare-cavia!
+                                                  with-before-after]]
+            [clojure.test :refer [deftest is]]))
+
+(defn- fixup-bam-aln [aln]
+  (-> aln
+      (dissoc :end)
+      (update :cigar #(if (= % "") "*" %))
+      (update :options #(sort-by (comp name key first) %))))
+
+(deftest reader-test
+  (with-open [bam-rdr (sam/reader common/test-bam-file)
+              cram-rdr (cram/reader common/test-cram-file
+                                    {:reference common/test-fa-file})
+              cram-rdr' (cram/reader cram-rdr)]
+    (is (= (sam/read-header bam-rdr)
+           (dissoc (cram/read-header cram-rdr) :HD)
+           (dissoc (cram/read-header cram-rdr') :HD)))
+    (is (= (sam/read-refs bam-rdr)
+           (cram/read-refs cram-rdr)
+           (cram/read-refs cram-rdr')))
+    (is (= (map fixup-bam-aln (sam/read-alignments bam-rdr))
+           (cram/read-alignments cram-rdr)
+           (cram/read-alignments cram-rdr')))))
+
+(deftest-remote reader-with-multiple-containers-test
+  (with-before-after {:before (prepare-cavia!)}
+    (with-open [bam-rdr (sam/reader common/medium-bam-file)
+                cram-rdr (cram/reader common/medium-cram-file
+                                      {:reference common/hg19-twobit-file})]
+      (is (= (sam/read-header bam-rdr)
+             (dissoc (cram/read-header cram-rdr) :HD)))
+      (is (= (sam/read-refs bam-rdr)
+             (cram/read-refs cram-rdr)))
+      (is (= (map fixup-bam-aln (sam/read-alignments bam-rdr))
+             (cram/read-alignments cram-rdr))))))

test/cljam/test_common.clj

@@ -32,7 +32,10 @@
   (expand-deftest (with-meta sym {:remote true}) args body))
 
 (defprofile mycavia
-  {:resources [{:id "large.bam"
+  {:resources [{:id "hg19.2bit"
+                :url "https://test.chrov.is/data/refs/hg19.2bit"
+                :sha1 "95e5806aee9ecc092d30a482aaa008ef66cbc468"}
+               {:id "large.bam"
                 :url "https://test.chrov.is/data/GSM721144_H3K36me3.nodup.bam"
                 :sha1 "ad282c3779120057abc274ad8fad1910a4ad867b"}
                {:id "large.bai"
@@ -162,6 +165,8 @@
 
 ;; ### CRAM file
 
+(def test-cram-file "test-resources/cram/test.cram")
+(def medium-cram-file "test-resources/cram/medium.cram")
 (def medium-with-standard-tags-cram-file "test-resources/cram/medium_with_standard_tags.cram")
 
 ;; ### FASTA files
@@ -187,6 +192,7 @@
 (def test-twobit-be-file "test-resources/twobit/be-test.2bit")
 (def test-twobit-be-n-file "test-resources/twobit/be-test-n.2bit")
 (def medium-twobit-file "test-resources/twobit/medium.2bit")
+(def hg19-twobit-file (cavia/resource mycavia "hg19.2bit"))
 
 ;; ### FASTQ files