Re-Ordering priority in SeekableStreamFactory

* Now when constructing streams it will prefer NIO plugins.
* If no http / ftp plugin exists it will fall back to the htsjdk bulit in
* No longer special casing local files, these will now be handled through NIO as well.
* Deprecating SeekableStreamFactory.isFilePath() since it is no longer used and interacts poorly
  with nio filesystem providers

src/main/java/htsjdk/samtools/seekablestream/SeekableStreamFactory.java

@@ -23,12 +23,17 @@
  */
 package htsjdk.samtools.seekablestream;
 
+import htsjdk.io.HtsPath;
+import htsjdk.io.IOPath;
 import htsjdk.samtools.util.IOUtil;
+import htsjdk.tribble.TribbleException;
+
 import java.io.File;
 import java.io.IOException;
 import java.net.URI;
 import java.net.URL;
 import java.nio.channels.SeekableByteChannel;
+import java.nio.file.Path;
 import java.util.function.Function;
 
 /**
@@ -61,9 +66,28 @@ public static ISeekableStreamFactory getInstance(){
      * Does this path point to a regular file on disk and not something like a URL?
      * @param path the path to test
      * @return true if the path is to a file on disk
+     * @deprecated this method is simplistic and no longer particularly useful since IOPath allows similar access to
+     * various non-file data sources, internal use has been replaced with {@link #isSpecialCase(String)}
      */
+    @Deprecated
     public static boolean isFilePath(final String path) {
-        return ! ( path.startsWith("http:") || path.startsWith("https:") || path.startsWith("ftp:") );
+        return !isSpecialCaseUrlType(path);
+    }
+
+    /**
+     * is this path being handled by one of the legacy SeekableStream types (http(s) / ftp)
+     *
+     * @param path a path to check
+     * @return if the path is not being handled by a FileSystemProvider and it can be read by legacy streams
+     */
+    public static boolean isSpecialCase(final String path){
+        return !new HtsPath(path).isPath()  //if we have a provider for it that's what we'll use
+                && isSpecialCaseUrlType(path); // otherwise we fall back to the special handlers
+    }
+
+    //is this onee of the url types that has legacy htsjdk support built in?
+    private static boolean isSpecialCaseUrlType(final String path) {
+        return path.startsWith("http:") || path.startsWith("https:") || path.startsWith("ftp:");
     }
 
     private static class DefaultSeekableStreamFactory implements ISeekableStreamFactory {
@@ -79,7 +103,7 @@ public SeekableStream getStreamFor(final String path) throws IOException {
         }
 
         /**
-         * The wrapper will only be applied to the stream if the stream is treated as a {@link java.nio.file.Path}
+         * The wrapper will only be applied to the stream if the stream is treated as a {@link Path}
          *
          * This currently means any uri with a scheme that is not http, https, ftp, or file will have the wrapper applied to it
          *
@@ -89,26 +113,30 @@ public SeekableStream getStreamFor(final String path) throws IOException {
         @Override
         public SeekableStream getStreamFor(final String path,
                                            Function<SeekableByteChannel, SeekableByteChannel> wrapper) throws IOException {
-            // todo -- add support for SeekableBlockInputStream
-
-            if (path.startsWith("http:") || path.startsWith("https:")) {
-                final URL url = new URL(path);
-                return new SeekableHTTPStream(url);
-            } else if (path.startsWith("ftp:")) {
-                return new SeekableFTPStream(new URL(path));
-            } else if (path.startsWith("file:")) {
-                try {
-                    // convert to URI in order to obtain a decoded version of the path string suitable
-                    // for use with the File constructor
-                    final String decodedPath = new URI(path).getPath();
-                    return new SeekableFileStream(new File(decodedPath));
-                } catch (java.net.URISyntaxException e) {
-                    throw new IllegalArgumentException(String.format("The input string %s contains a URI scheme but is not a valid URI", path), e);
-                }
-            } else if (IOUtil.hasScheme(path)) {
-                return new SeekablePathStream(IOUtil.getPath(path), wrapper);
+            return getStreamFor(new HtsPath(path), wrapper);
+        }
+
+
+        /**
+         * The wrapper will only be applied to the stream if the stream is treated as a non file:// {@link Path}
+         *
+         * This has a fall back to htsjdk's built in http and ftp providers if no FileSystemProvder is available for them
+         *
+         * @param path    an IOPath to be opened
+         * @param wrapper a wrapper to apply to the stream allowing direct transformations on the byte stream to be applied
+         * @throws IOException
+         */
+        public static SeekableStream getStreamFor(final IOPath path, Function<SeekableByteChannel, SeekableByteChannel> wrapper) throws IOException {
+            if(path.isPath()) {
+                return path.getScheme().equals("file")
+                        ? new SeekablePathStream(path.toPath()) //don't apply the wrapper to local files
+                        : new SeekablePathStream(path.toPath(), wrapper);
             } else {
-                return new SeekableFileStream(new File(path));
+               return switch(path.getScheme()){
+                   case "http", "https" -> new SeekableHTTPStream(new URL(path.getURIString()));
+                   case "ftp" -> new SeekableFTPStream((new URL(path.getURIString())));
+                   default -> throw new TribbleException("Unknown path type. No FileSystemProvider available for " + path.getRawInputString());
+               };
             }
         }
 

src/main/java/htsjdk/tribble/FeatureCodec.java

@@ -18,6 +18,7 @@
 
 package htsjdk.tribble;
 
+import htsjdk.io.IOPath;
 import htsjdk.samtools.util.LocationAware;
 import htsjdk.tribble.index.tabix.TabixFormat;
 

src/main/java/htsjdk/tribble/TribbleIndexedFeatureReader.java

@@ -23,6 +23,7 @@
  */
 package htsjdk.tribble;
 
+import htsjdk.io.HtsPath;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.seekablestream.SeekableStreamFactory;
 import htsjdk.samtools.util.IOUtil;
@@ -40,6 +41,7 @@
 import java.net.URI;
 import java.net.URLEncoder;
 import java.nio.channels.SeekableByteChannel;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -60,9 +62,9 @@ public class TribbleIndexedFeatureReader<T extends Feature, SOURCE> extends Abst
     private Index index;
 
     /**
-     * is the path pointing to our source data a regular file?
+     * is the path backed by old style built in http(s) / ftp support instead of a FileSystemProvider
      */
-    private final boolean pathIsRegularFile;
+    private final boolean pathIsOldStyleHttpOrFtp;
 
     /**
      * a potentially reusable seekable stream for queries over regular files
@@ -97,8 +99,7 @@ public TribbleIndexedFeatureReader(final String featurePath, final FeatureCodec<
             }
         }
 
-        // does path point to a regular file?
-        this.pathIsRegularFile = SeekableStreamFactory.isFilePath(path);
+        this.pathIsOldStyleHttpOrFtp = SeekableStreamFactory.isSpecialCase(path);
 
         readHeader();
     }
@@ -203,7 +204,7 @@ private SeekableStream getSeekableStream() throws IOException {
      * @return true if
      */
     private boolean reuseStreamInQuery() {
-        return pathIsRegularFile;
+        return !pathIsOldStyleHttpOrFtp;
     }
 
     @Override
@@ -252,7 +253,7 @@ private void readHeader() throws IOException {
         PositionalBufferedStream pbs = null;
         try {
             is = ParsingUtils.openInputStream(path, wrapper);
-            if (IOUtil.hasBlockCompressedExtension(new URI(URLEncoder.encode(path, "UTF-8")))) {
+            if (IOUtil.hasBlockCompressedExtension(new URI(URLEncoder.encode(path, StandardCharsets.UTF_8)))) {
                 // TODO: TEST/FIX THIS! https://github.com/samtools/htsjdk/issues/944
                 // TODO -- warning I don't think this can work, the buffered input stream screws up position
                 is = new GZIPInputStream(new BufferedInputStream(is));

src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java

@@ -17,13 +17,28 @@
 public class SeekableStreamFactoryTest extends HtsjdkTest {
     private static final File TEST_DATA_DIR = new File("src/test/resources/htsjdk/samtools");
 
-    @Test
-    public void testIsFilePath() {
-        Assert.assertEquals(SeekableStreamFactory.isFilePath("x"), true);
-        Assert.assertEquals(SeekableStreamFactory.isFilePath(""), true);
-        Assert.assertEquals(SeekableStreamFactory.isFilePath("http://broadinstitute.org"), false);
-        Assert.assertEquals(SeekableStreamFactory.isFilePath("https://broadinstitute.org"), false);
-        Assert.assertEquals(SeekableStreamFactory.isFilePath("ftp://broadinstitute.org"), false);
+    @DataProvider
+    public Object[][] getSpecialCasePaths(){
+        return new Object[][]{
+                {"x", true},
+                {"", true},
+                {"http://broadinstitute.org", false},
+                {"https://broadinstitute.org", false},
+                {"ftp://broadinstitute.org", false}
+        };
+    }
+
+    @Test(dataProvider = "getSpecialCasePaths")
+    public void testIsFilePath(String path, boolean expected) {
+        Assert.assertEquals(SeekableStreamFactory.isFilePath(path), expected);
+    }
+
+
+    // this test isn't particularly useful since we're not testing the meaninful case of having the http-nio provider
+    // installed
+    @Test(dataProvider = "getSpecialCasePaths")
+    public void testIsSpecialCase(String path, boolean expected) {
+        Assert.assertEquals(SeekableStreamFactory.isSpecialCase(path), ! expected);
     }
 
     @DataProvider(name="getStreamForData")