Reject piped input (/dev/stdin) for BedToIntervalList

broadinstitute · Nov 14, 2023 · a62843d · a62843d
1 parent 5721517
commit a62843d
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/src/main/java/picard/util/BedToIntervalList.java b/src/main/java/picard/util/BedToIntervalList.java
@@ -24,6 +24,7 @@
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.IntervalsManipulationProgramGroup;
+import picard.nio.PicardHtsPath;
 
 import java.io.File;
 import java.io.IOException;
@@ -116,6 +117,11 @@ protected int doWork() {
         IOUtil.assertFileIsReadable(INPUT);
         IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);
         IOUtil.assertFileIsWritable(OUTPUT);
+
+        if(PicardHtsPath.isOther(new PicardHtsPath(INPUT))) {
+            throw new IllegalArgumentException("BedToIntervalList cannot read from /dev/stdin.");
+        }
+
         try {
             // create a new header that we will assign the dictionary provided by the SAMSequenceDictionaryExtractor to.
             final SAMFileHeader header = new SAMFileHeader();