Reject piped input (/dev/stdin) for BedToIntervalList (#1918)

* Reject piped input (/dev/stdin) for BedToIntervalList

* Directly compare INPUT to /dev/stdin instead of PicardHtsPath.isOther()

* Update error message and add a test.

---------

Co-authored-by: Chris Norman <cnorman@broadinstitute.org>

src/main/java/picard/util/BedToIntervalList.java

@@ -118,8 +118,13 @@ public class BedToIntervalList extends CommandLineProgram {
  @Override
  protected int doWork() {
  IOUtil.assertFileIsReadable(INPUT);
+ if(INPUT.getPath().equals("/dev/stdin")) {
+ throw new IllegalArgumentException("BedToIntervalList does not support reading from standard input - a file must be provided.");
+ }
+
  IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);
  IOUtil.assertFileIsWritable(OUTPUT);
+
  try {
  // create a new header that we will assign the dictionary provided by the SAMSequenceDictionaryExtractor to.
  final SAMFileHeader header = new SAMFileHeader();

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[][]{