Merge pull request #478 from nenewell/master

#259 - replace calls to getChr() with getContig(). Closes #478
broadinstitute · May 2, 2015 · 20e430d · 20e430d
2 parents 3dba570 + e6feb6a
commit 20e430d
Showing 1 changed file with 6 additions and 7 deletions.
diff --git a/src/test/java/org/broadinstitute/hellbender/utils/codecs/table/TableCodecUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/codecs/table/TableCodecUnitTest.java
@@ -54,12 +54,12 @@ public void testGoodNames(String goodName){
     @Test
     public void testChrs(){
         TableCodec tc = new TableCodec();
-        Assert.assertEquals(tc.decode("1:1  1   2   3").getChr(), "1");
-        Assert.assertEquals(tc.decode("chr1:1  1   2   3").getChr(), "chr1");
-        Assert.assertEquals(tc.decode("1:1+  1   2   3").getChr(), "1");
-        Assert.assertEquals(tc.decode("1  1   2   3").getChr(), "1");
-        Assert.assertEquals(tc.decode("fred  1   2   3").getChr(), "fred");
-        Assert.assertEquals(tc.decode("2:1,000  1   2   3").getChr(), "2");
+        Assert.assertEquals(tc.decode("1:1  1   2   3").getContig(), "1");
+        Assert.assertEquals(tc.decode("chr1:1  1   2   3").getContig(), "chr1");
+        Assert.assertEquals(tc.decode("1:1+  1   2   3").getContig(), "1");
+        Assert.assertEquals(tc.decode("1  1   2   3").getContig(), "1");
+        Assert.assertEquals(tc.decode("fred  1   2   3").getContig(), "fred");
+        Assert.assertEquals(tc.decode("2:1,000  1   2   3").getContig(), "2");
     }
 
     @DataProvider(name = "dataLines")
@@ -111,7 +111,6 @@ public void testDecodeHeader2(){
         Assert.assertEquals(decode.get("c"), "3");
         Assert.assertEquals(decode.getLocation().getContig(), "1");
         Assert.assertEquals(decode.getContig(), "1");
-        Assert.assertEquals(decode.getChr(), "1");
         Assert.assertEquals(decode.getLocation().getStart(), 1);
         Assert.assertEquals(decode.getLocation().getEnd(), 1);
     }