Fixed bug disallowing file-based index and seekable path based source

src/main/java/htsjdk/samtools/SamReaderFactory.java

@@ -316,7 +316,7 @@ public SamReader open(final SamInputResource resource) {
                             final SeekableStream indexSeekable = indexMaybe == null ? null : indexMaybe.asUnbufferedSeekableStream();
                             // do not close bufferedStream, it's the same stream we're getting here.
                             SeekableStream sourceSeekable = data.asUnbufferedSeekableStream();
-                            if (indexFile!=null || null == sourceSeekable || null == indexSeekable) {
+                            if (null == sourceSeekable || null == indexSeekable) {
                                 // not seekable.
                                 // it's OK that we consumed a bit of the stream already, this ctor expects it.
                                 primitiveSamReader = new BAMFileReader(bufferedStream, indexFile, false, asynchronousIO, validationStringency, this.samRecordFactory);
@@ -326,7 +326,7 @@ public SamReader open(final SamInputResource resource) {
                                 // and read a bit from, and that form of the ctor expects the stream to start at 0.
                                 sourceSeekable.seek(0);
                                 primitiveSamReader = new BAMFileReader(
-                                    sourceSeekable, indexSeekable, false, asynchronousIO, validationStringency, this.samRecordFactory);
+                                        sourceSeekable, indexSeekable, false, asynchronousIO, validationStringency, this.samRecordFactory);
                             }
                         } else {
                             bufferedStream.close();

src/test/java/htsjdk/samtools/SamReaderFactoryTest.java

@@ -284,7 +284,43 @@ public void queryInputResourcePermutation(final SamInputResource resource) throw
         }
         reader.close();
     }
-    
+
+
+    /**
+     * A path that pretends it's not based upon a file.  This helps in cases where we want to test branches
+     * that apply to non-file based paths without actually having to use non-file based resources (like cloud urls)
+     */
+    private static class NeverFilePathInputResource extends PathInputResource {
+        public NeverFilePathInputResource(Path pathResource) {
+            super(pathResource);
+        }
+
+        @Override
+        public File asFile() {
+            return null;
+        }
+    }
+
+    @Test
+    public void checkHasIndexForStreamingPathBamWithFileIndex() throws IOException {
+        InputResource bam = new NeverFilePathInputResource(localBam.toPath());
+        InputResource index = new FileInputResource(localBamIndex);
+
+        // ensure that the index is being used, not checked in queryInputResourcePermutation
+        try (final SamReader reader = SamReaderFactory.makeDefault().open(new SamInputResource(bam, index))) {
+            Assert.assertTrue(reader.hasIndex());
+        }
+    }
+
+    @Test
+    public void queryStreamingPathBamWithFileIndex() throws IOException {
+        InputResource bam = new NeverFilePathInputResource(localBam.toPath());
+        InputResource index = new FileInputResource(localBamIndex);
+
+        final SamInputResource resource = new SamInputResource(bam, index);
+        queryInputResourcePermutation(new SamInputResource(bam, index));
+    }
+
     @Test
     public void customReaderFactoryTest() throws IOException {
         try {