Fixing bad behavior in IOUtil.deletePaths

src/main/java/htsjdk/samtools/util/DiskBackedQueue.java

@@ -339,7 +339,7 @@ private E readFileRecord (final Path file) {
     private void closeIOResources() {
         CloserUtil.close(this.outputStream);
         CloserUtil.close(this.inputStream);
-        if (this.diskRecords != null) IOUtil.deletePaths(this.diskRecords);
+        if (this.diskRecords != null) IOUtil.deletePath(this.diskRecords);
     }
 
     /**

src/main/java/htsjdk/samtools/util/IOUtil.java

@@ -303,16 +303,33 @@ public static void deleteFiles(final Iterable<File> files) {
     }
 
     public static void deletePaths(final Path... paths) {
-        deletePaths(Arrays.asList(paths));
+        for(Path path: paths){
+            deletePath(path);
+        }
     }
 
+    /**
+     * Iterate through Paths and delete each one.
+     * Note: Path is itself an Iterable<Path>.  This method special cases that and deletes the single Path rather than
+     * Iterating the Path for targets to delete.
+     * @param paths an iterable of Paths to delete
+     */
     public static void deletePaths(final Iterable<Path> paths) {
-        for (final Path p : paths) {
-            try {
-                Files.delete(p);
-            } catch (IOException e) {
-                System.err.println("Could not delete file " + p);
-            }
+        //Path is itself an Iterable<Path> which causes very confusing behavior if we don't explicitly check here.
+        if( paths instanceof Path){
+            deletePath((Path)paths);
+        }
+        paths.forEach(IOUtil::deletePath);
+    }
+
+    /**
+     * Attempt to delete a single path and log an error if it is not deleted.
+     */
+    public static void deletePath(Path path){
+        try {
+            Files.delete(path);
+        } catch (IOException e) {
+            System.err.println("Could not delete file " + path);
         }
     }
 

src/test/java/htsjdk/samtools/util/IOUtilTest.java

@@ -35,7 +35,6 @@
 import java.nio.file.Paths;
 import java.nio.file.spi.FileSystemProvider;
 
-import htsjdk.samtools.BamFileIoUtils;
 import htsjdk.samtools.SAMException;
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
@@ -44,15 +43,12 @@
 import org.testng.annotations.Test;
 
 import java.lang.IllegalArgumentException;
-import java.nio.file.Path;
-import java.nio.file.Files;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 import java.util.stream.Collectors;
 import java.util.Random;
-import java.util.stream.Stream;
 import java.util.zip.GZIPOutputStream;
 
 
@@ -318,13 +314,29 @@ public void testGetDefaultTmpDirPath() throws Exception {
     public void testDeletePathLocal(final List<String> fileNames) throws Exception {
         final File tmpDir = IOUtil.createTempDir("testDeletePath", "");
         final List<Path> paths = createLocalFiles(tmpDir, fileNames);
-        testDeletePath(paths);
+        testDeletePaths(paths);
+    }
+
+    @Test
+    public void testDeleteSinglePath() throws Exception {
+        final Path toDelete = Files.createTempFile("file",".bad");
+        Assert.assertTrue(Files.exists(toDelete));
+        IOUtil.deletePath(toDelete);
+        Assert.assertFalse(Files.exists(toDelete));
+    }
+
+    @Test
+    public void testDeleteSingleWithDeletePaths() throws Exception {
+        final Path toDelete = Files.createTempFile("file",".bad");
+        Assert.assertTrue(Files.exists(toDelete));
+        IOUtil.deletePaths(toDelete);
+        Assert.assertFalse(Files.exists(toDelete));
     }
 
     @Test(dataProvider = "fileNamesForDelete")
     public void testDeletePathJims(final List<String> fileNames) throws Exception {
         final List<Path> paths = createJimfsFiles("testDeletePath", fileNames);
-        testDeletePath(paths);
+        testDeletePaths(paths);
     }
 
     @Test(dataProvider = "fileNamesForDelete")
@@ -340,7 +352,8 @@ public void testDeleteArrayPathJims(final List<String> fileNames) throws Excepti
         testDeletePathArray(paths);
     }
 
-    private static void testDeletePath(final List<Path> paths) {
+
+    private static void testDeletePaths(final List<Path> paths) {
         paths.forEach(p -> Assert.assertTrue(Files.exists(p)));
         IOUtil.deletePaths(paths);
         paths.forEach(p -> Assert.assertFalse(Files.exists(p)));