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 <[email protected]>
broadinstitute · Mar 12, 2024 · 5b0b4c0 · 5b0b4c0
1 parent 6fe8547
commit 5b0b4c0
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diff --git a/src/main/java/picard/util/BedToIntervalList.java b/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();

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[][]{