From 4c1c7660e55c7268366060e745e9657a53c4db95 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@broadinstitute.org>
Date: Wed, 2 Oct 2024 16:52:54 +0200
Subject: [PATCH] SamReaderFactory opens non-regular File and Path the same way
 (#1717)

---
 src/main/java/htsjdk/samtools/SamReaderFactory.java   |  4 +++-
 .../java/htsjdk/samtools/SamReaderFactoryTest.java    | 11 +++++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/main/java/htsjdk/samtools/SamReaderFactory.java b/src/main/java/htsjdk/samtools/SamReaderFactory.java
index 0a30ecd5ef..e93a2cd392 100644
--- a/src/main/java/htsjdk/samtools/SamReaderFactory.java
+++ b/src/main/java/htsjdk/samtools/SamReaderFactory.java
@@ -100,7 +100,9 @@ public SamReader open(final Path path) {
     public SamReader open(final Path path,
             Function<SeekableByteChannel, SeekableByteChannel> dataWrapper,
             Function<SeekableByteChannel, SeekableByteChannel> indexWrapper) {
-        final SamInputResource r = SamInputResource.of(path, dataWrapper);
+        final SamInputResource r = dataWrapper == null
+                ? SamInputResource.of(path)
+                : SamInputResource.of(path, dataWrapper);
         final Path indexMaybe = SamFiles.findIndex(path);
         if (indexMaybe != null) r.index(indexMaybe, indexWrapper);
         return open(r);
diff --git a/src/test/java/htsjdk/samtools/SamReaderFactoryTest.java b/src/test/java/htsjdk/samtools/SamReaderFactoryTest.java
index 3a50c93851..9a2be957e0 100644
--- a/src/test/java/htsjdk/samtools/SamReaderFactoryTest.java
+++ b/src/test/java/htsjdk/samtools/SamReaderFactoryTest.java
@@ -333,6 +333,17 @@ public void openPath() throws IOException {
         }
     }
 
+    @Test
+    public void testOpenIrregularPath() throws IOException {
+        // See: htsjdk.samtools.SamInputResource.of(java.nio.file.Path)
+        // Related to https://github.com/samtools/htsjdk/issues/1716
+        final File irregularFile = new File("/dev/null");
+        try (final SamReader fileReader = SamReaderFactory.makeDefault().open(irregularFile);
+             final SamReader pathReader = SamReaderFactory.makeDefault().open(irregularFile.toPath())) {
+            Assert.assertEquals(fileReader.getResourceDescription(), pathReader.getResourceDescription());
+        }
+    }
+
     @DataProvider(name = "URIFallbackProvider")
     public Object[][] URIFallbackProvider() throws MalformedURLException {
         return new Object[][]{