Add test for cljam level

ayamada · Apr 27, 2017 · a134664 · a134664
1 parent 11a0fef
commit a134664
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Showing 2 changed files with 21 additions and 3 deletions.
diff --git a/test/cljam/t_cli.clj b/test/cljam/t_cli.clj
@@ -2,7 +2,9 @@
   (:require [clojure.test :refer :all]
             [cljam.t-common :refer :all]
             [clojure.java.io :as io]
-            [cljam.cli :as cli])
+            [cljam.cli :as cli]
+            [cljam.io :as cio]
+            [cljam.bam :as bam])
   (:import [java.io PrintStream]))
 
 (defmacro with-out-file
@@ -132,8 +134,10 @@
                  (with-out-file temp-out (cli/level [test-bam-file temp-bam]))))
     (is (not-throw? (with-out-file temp-out (cli/level [test-sorted-bam-file
                                                         temp-bam]))))
-    ;; TODO: examine contents of temp-bam
-    ))
+    (with-open [rdr (bam/reader temp-bam :ignore-index true)]
+      (is (= (map #(first (keep :LV (:options %)))
+                  (cio/read-alignments rdr))
+             test-sorted-bam-levels)))))
 
 (deftest about-run
   (with-before-after {:before (prepare-cache!)

diff --git a/test/cljam/t_common.clj b/test/cljam/t_common.clj
@@ -307,6 +307,20 @@
    {:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30], :size 75}
    {:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30], :size 74}])
 
+(def test-sorted-bam-levels
+  [{:type "i", :value 0}
+   {:type "i", :value 1}
+   {:type "i", :value 2}
+   {:type "i", :value 2}
+   {:type "i", :value 0}
+   {:type "i", :value 0}
+   {:type "i", :value 0}
+   {:type "i", :value 1}
+   {:type "i", :value 2}
+   {:type "i", :value 3}
+   {:type "i", :value 4}
+   {:type "i", :value 5}])
+
 (def test-fa
   [{:rname "ref",  :offset 5,  :seq "AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT", :blen 45}
    {:rname "ref2", :offset 57, :seq "aggttttataaaacaattaagtctacagagcaactacgcg",      :blen 40}])