Remove Files.exist from the .of(Path) method in SamInputResource (#1128)

* According to @drozen: "This operation is expensive over certain NIO filesystems (eg., takes on the order of seconds over GCS), so forcing it at reader creation time could potentially add hours to the wall-clock time of a task that needed to access many bams over GCS."

Author: Yossi Farjoun

src/main/java/htsjdk/samtools/SamInputResource.java

@@ -38,6 +38,7 @@
 import java.net.URL;
 import java.nio.channels.SeekableByteChannel;
 import java.nio.file.FileSystemNotFoundException;
+import java.nio.file.FileSystems;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.function.Function;
@@ -93,17 +94,22 @@ public static SamInputResource of(final File file) {
     /** Creates a {@link SamInputResource} reading from the provided resource, with no index. */
     public static SamInputResource of(final Path path) {
 
-        if (Files.isRegularFile(path) &&  Files.exists(path)) {
-            return new SamInputResource(new PathInputResource(path));
-        } else {
-            // in the case of named pipes and other non-seekable paths there's a bug in the implementation of
-            // java's GZIPInputStream which inappropriately uses .available() and then gets confused with the result
-            // of 0. For reference see:
-            // https://bugs.java.com/view_bug.do?bug_id=7036144
-            // https://github.com/samtools/htsjdk/pull/1077
-            // https://github.com/samtools/htsjdk/issues/898
+        // in the case of named pipes and other non-seekable paths there's a bug in the implementation of
+        // java's GZIPInputStream which inappropriately uses .available() and then gets confused with the result
+        // of 0. For reference see:
+        // https://bugs.java.com/view_bug.do?bug_id=7036144
+        // https://github.com/samtools/htsjdk/pull/1077
+        // https://github.com/samtools/htsjdk/issues/898
+
+        // This still doesn't support the case where someone is creating a named pipe in a non-default
+        // file system and then using it as input and passing a GZIPed into the other end of the pipe.
 
+        // To work around this bug, we fall back to using a FileInputResource rather than a PathInputResource
+        // when we encounter a non-regular file using the default NIO filesystem (file://)
+        if (path.getFileSystem() == FileSystems.getDefault() && !Files.isRegularFile(path)) {
             return of(path.toFile());
+        } else {
+            return new SamInputResource(new PathInputResource(path));
         }
     }