fix(qsv): adding forgotten test file

Committing test file that was not included in previous commit.

Author: newellf

qsv/test/org/qcmg/qsv/discordantpair/MatePairsReaderTest.java

@@ -21,7 +21,8 @@ public class MatePairsReaderTest {
     private MatePairsReader reader;
     private File matePairDir;
     private static final String FILE_SEPERATOR = System.getProperty("file.separator");
-    private String fileName = "chr7_test_TD_AAC";
+    private String fileName = "chr7_xxx_test_TD_AAC";
+    private String fileNameChrUn = "chrUn_KI270438v1_xxx_test_TD_AAC";
 
     @Rule
     public TemporaryFolder testFolder = new TemporaryFolder();
@@ -30,11 +31,16 @@ public class MatePairsReaderTest {
     public void setUp() throws IOException, QSVException {
        matePairDir = testFolder.newFolder("matepair");
        TestUtil.createTmpClusterFile(matePairDir.getAbsolutePath() + FILE_SEPERATOR, PairClassification.AAC, fileName);
+       TestUtil.createTmpClusterChrUnFile(matePairDir.getAbsolutePath() + FILE_SEPERATOR, PairClassification.AAC, fileNameChrUn);
+
        reader = new MatePairsReader(PairGroup.AAC, matePairDir.getAbsolutePath() + FILE_SEPERATOR, fileName, "TD");
    	   assertNotNull(reader.getFilesToRead());
    	   assertNotNull(reader.getFilesToRead().get("chr7"));
    	   assertEquals(1, reader.getFilesToRead().get("chr7").size());
    	   assertEquals(fileName, reader.getFilesToRead().get("chr7").getFirst().getName());
+       assertNotNull(reader.getFilesToRead().get("chrUn_KI270438v1"));
+       assertEquals(1, reader.getFilesToRead().get("chrUn_KI270438v1").size());
+       assertEquals(fileNameChrUn, reader.getFilesToRead().get("chrUn_KI270438v1").getFirst().getName());
     }
 
     @After
@@ -55,4 +61,14 @@ public void testReadInPairs() throws Exception {
        assertEquals("1789_1456_806:20110221052813657", list.get(0).getReadName());
     }
 
+    @Test
+    public void testReadInChrUnPairs() throws Exception {
+        List<File> files = new ArrayList<File>();
+        files.add(new File(matePairDir.getAbsolutePath() + FILE_SEPERATOR + "AAC" + FILE_SEPERATOR + fileNameChrUn));
+        List<MatePair> list = reader.getMatePairsListByFiles(files, true);
+
+        assertEquals(4, list.size());
+        assertEquals("H3HHCALXX:2:1105:3188332:0:07262735-323a-489b-bd6d-10dcdc6726d0", list.get(0).getReadName());
+    }
+
 }