Merge pull request #69 from ayamada/feature/tune-cloverage-worktime

For reduce worktime of `lein cloverage`
chrovis · Apr 28, 2017 · f6ec43b · f6ec43b
2 parents 11a0fef + 878f0fd
commit f6ec43b
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Showing 3 changed files with 23 additions and 16 deletions.
diff --git a/test/cljam/t_bam.clj b/test/cljam/t_bam.clj
@@ -100,7 +100,7 @@
     (is (thrown? IOException (bam/reader invalid-file-2 :ignore-index true)))
     (is (thrown? IOException (bam/reader not-found-file :ignore-index true)))))
 
-(deftest bamreader-medium-file
+(deftest-slow bamreader-medium-file
   (with-before-after {:before (prepare-cache!)
                       :after (clean-cache!)}
     (with-open [rdr (bam/reader medium-bam-file :ignore-index true)]

diff --git a/test/cljam/t_bam_indexer.clj b/test/cljam/t_bam_indexer.clj
@@ -9,6 +9,7 @@
             [cljam.bam-indexer :as bai]))
 
 (def temp-file-sorted (str temp-dir "/test.sorted.bam"))
+(def temp-file-sorted-2 (str temp-dir "/test.sorted2.bam"))
 
 (deftest about-bam-indexer
   (with-before-after {:before (do (prepare-cache!)
@@ -52,23 +53,29 @@
       )))
 
 (deftest about-bam-indexer-small-file
-  (doseq [n-threads [1 4]]
-    (with-before-after {:before (do (prepare-cache!)
-                                    (fs/copy small-bam-file temp-file-sorted))
-                        :after (clean-cache!)}
+  (with-before-after {:before (do (prepare-cache!)
+                                  (fs/copy small-bam-file temp-file-sorted)
+                                  (fs/copy small-bam-file temp-file-sorted-2))
+                      :after (clean-cache!)}
+    (let [temp-file-sorted-bai (str temp-file-sorted ".bai")
+          temp-file-sorted-bai-2 (str temp-file-sorted-2 ".bai")]
       (is (not-throw? (bai/create-index temp-file-sorted
-                                        (str temp-file-sorted ".bai")
-                                        :n-threads n-threads)))
-      (is (fs/exists? (str temp-file-sorted ".bai")))
+                                        temp-file-sorted-bai
+                                        :n-threads 1)))
+      (is (fs/exists? temp-file-sorted-bai))
+      (is (not-throw? (bai/create-index temp-file-sorted-2
+                                        temp-file-sorted-bai-2
+                                        :n-threads 4)))
+      (is (fs/exists? temp-file-sorted-bai-2))
+      (is (same-file? temp-file-sorted-bai temp-file-sorted-bai-2))
       (with-open [r (bam/reader temp-file-sorted)]
         ;; Random read with different number of spans.
         (are [?param ?counts] (= (count (io/read-alignments r ?param)) ?counts)
-          {:chr "chr1" :start 23000000 :end 25000000 :depth :shallow} 14858
-          {:chr "chr1" :start 23000000 :end 25000000 :depth :pointer} 14858
-          {:chr "chr1" :start 23000000 :end 25000000 :depth :deep} 14858
-          {:chr "chr1" :start 23000000 :end 24500000 :depth :deep} 11424
-          {:chr "chr1" :start 23000000 :end 24000000 :depth :deep} 10010
-          {:chr "chr1" :start 23000000 :end 23500000 :depth :deep} 3806
+          {:chr "chr1" :start 23000000 :end 23001000 :depth :deep} 46 ;; 1 span
+          {:chr "chr1" :start 24900000 :end 24902000 :depth :deep} 3  ;; 2 spans
+          {:chr "chr1" :start 24000000 :end 24001000 :depth :deep} 6  ;; 3 spans
+          {:chr "chr1" :start 23260000 :end 23268650 :depth :deep} 58 ;; 4 spans
+          {:chr "chr1" :start 23430000 :end 23470000 :depth :deep} 55 ;; 5 spans
           {:chr "*"} 0)))))
 
 (deftest-slow about-bam-indexer-medium-file

diff --git a/test/cljam/t_pileup.clj b/test/cljam/t_pileup.clj
@@ -84,8 +84,8 @@
               (mplp/pileup-seq 101 120 (map #(hash-map :pos (inc %) :cigar "10M") (range))))
          [10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10]))
   (is (= (map :pos
-              (last (mplp/pileup-seq 1 1000000 (map #(hash-map :pos (inc %) :cigar "10M") (range)))))
-         [999991 999992 999993 999994 999995 999996 999997 999998 999999 1000000]))
+              (last (mplp/pileup-seq 1 100000 (map #(hash-map :pos (inc %) :cigar "10M") (range)))))
+         [99991 99992 99993 99994 99995 99996 99997 99998 99999 100000]))
 
   ;;     -----
   ;;    ----