Add tests for BAM random read with multiple spans.

chrovis · Jan 19, 2017 · f14f070 · f14f070
1 parent 09456cd
commit f14f070
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diff --git a/test-resources/small.bam b/test-resources/small.bam
diff --git a/test-resources/small.bam.bai b/test-resources/small.bam.bai
diff --git a/test/cljam/t_bam_indexer.clj b/test/cljam/t_bam_indexer.clj
@@ -46,6 +46,20 @@
       ;; (it will use https://gitlab.xcoo.jp/chrovis/cljam/issues/8 later)
       )))
 
+(with-state-changes [(before :facts (do (prepare-cache!)
+                                        (fs/copy small-bam-file temp-file-sorted)))
+                     (after :facts (clean-cache!))]
+  (fact "about BAM indexer (small file)"
+    (bai/create-index
+     temp-file-sorted (str temp-file-sorted ".bai")) => anything
+    (fs/exists? (str temp-file-sorted ".bai")) => truthy
+    (with-open [r (bam/reader temp-file-sorted)]
+      ;; Random read with different number of spans.
+      (count (io/read-alignments r {:chr "chr1" :start 23000000 :end 25000000 :depth :deep})) => 14858
+      (count (io/read-alignments r {:chr "chr1" :start 23000000 :end 24500000 :depth :deep})) => 11424
+      (count (io/read-alignments r {:chr "chr1" :start 23000000 :end 24000000 :depth :deep})) => 10010
+      (count (io/read-alignments r {:chr "chr1" :start 23000000 :end 23500000 :depth :deep})) => 3806)))
+
 (with-state-changes [(before :facts (do (prepare-cache!)
                                         (fs/copy medium-bam-file
                                                  temp-file-sorted)))

diff --git a/test/cljam/t_common.clj b/test/cljam/t_common.clj
@@ -63,6 +63,7 @@
 
 (def test-bam-file "test-resources/test.bam")
 (def test-sorted-bam-file "test-resources/test.sorted.bam")
+(def small-bam-file "test-resources/small.bam")
 (def medium-bam-file "test-resources/medium.bam")
 (def large-bam-file (cavia/resource mycavia "large.bam"))