add tests for SAM files that corrupt with adam + htsjdk 0.20.x (#120)

disq-bio · Sep 12, 2019 · 65cfd22 · 65cfd22
1 parent 8dd2362
commit 65cfd22
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diff --git a/src/test/java/org/disq_bio/disq/HtsjdkReadsRddTest.java b/src/test/java/org/disq_bio/disq/HtsjdkReadsRddTest.java
@@ -550,4 +550,24 @@ public void testEnableBAIAndSBI() throws Exception {
     Assert.assertTrue(
         Files.exists(Paths.get(URI.create(outputPath + SbiWriteOption.getIndexExtension()))));
   }
+
+  @Test
+  public void testCorruptedReadNameSAM() throws Exception {
+    String inputPath = getPath("small.sam");
+    HtsjdkReadsRddStorage htsjdkReadsRddStorage = HtsjdkReadsRddStorage.makeDefault(jsc);
+    HtsjdkReadsRdd htsjdkReadsRdd = htsjdkReadsRddStorage.read(inputPath);
+    SAMRecord record = htsjdkReadsRdd.getReads().first();
+    Assert.assertEquals("1", record.getReferenceName());
+    Assert.assertEquals(26472784, record.getStart());
+    Assert.assertEquals("simread:1:26472783:false", record.getReadName());
+  }
+
+  @Test
+  public void testCorruptedHeaderSAM() throws Exception {
+    String inputPath = getPath("flag-values.sam");
+    HtsjdkReadsRddStorage htsjdkReadsRddStorage = HtsjdkReadsRddStorage.makeDefault(jsc);
+    HtsjdkReadsRdd htsjdkReadsRdd = htsjdkReadsRddStorage.read(inputPath);
+    SAMRecord record = htsjdkReadsRdd.getReads().first();
+    Assert.assertEquals("read:0", record.getReadName());
+  }
 }