Update error message and add a test.

broadinstitute · Mar 12, 2024 · ccdbb90 · ccdbb90
1 parent b492efb
commit ccdbb90
Show file tree

Hide file tree

Showing 2 changed files with 13 additions and 1 deletion.
diff --git a/src/main/java/picard/util/BedToIntervalList.java b/src/main/java/picard/util/BedToIntervalList.java
@@ -119,7 +119,7 @@ public class BedToIntervalList extends CommandLineProgram {
     protected int doWork() {
         IOUtil.assertFileIsReadable(INPUT);
         if(INPUT.getPath().equals("/dev/stdin")) {
-            throw new IllegalArgumentException("BedToIntervalList cannot read from /dev/stdin.");
+            throw new IllegalArgumentException("BedToIntervalList does not support reading from standard input - a file must be provided.");
         }
 
         IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);

diff --git a/src/test/java/picard/util/BedToIntervalListTest.java b/src/test/java/picard/util/BedToIntervalListTest.java
@@ -61,6 +61,18 @@ public void testLengthZeroIntervalsSkipped(final String inputBed) throws IOExcep
         doTest(inputBed, "header.sam", false);
     }
 
+    @Test(expectedExceptions = IllegalArgumentException.class)
+    public void testRejectStdin() throws IOException {
+        final BedToIntervalList program = new BedToIntervalList();
+        final File outputFile  = File.createTempFile("bed_to_interval_list_test.", ".interval_list");
+        outputFile.deleteOnExit();
+        program.OUTPUT = outputFile;
+        program.SEQUENCE_DICTIONARY = new File(TEST_DATA_DIR, "header.sam");
+        program.UNIQUE = true;
+        program.INPUT = new File("/dev/stdin");
+        program.doWork();
+    }
+
     @DataProvider
     public Object[][] testBedToIntervalListDataProvider() {
         return new Object[][]{