Enable use of cloud reference files

src/main/java/picard/cmdline/CommandLineProgram.java

@@ -55,6 +55,7 @@
 import picard.cmdline.argumentcollections.ReferenceArgumentCollection;
 import picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection;
 import picard.nio.PathProvider;
+import picard.nio.PicardHtsPath;
 import picard.util.RExecutor;
 
 import java.io.File;
@@ -333,7 +334,15 @@ protected boolean parseArgs(final String[] argv) {
         if (!ret) {
             return false;
         }
-        REFERENCE_SEQUENCE = referenceSequence.getReferenceFile();
+
+        // Set the REFERENCE_SEQUENCE for tools that are not nio-aware and still depend on a File object
+        // (as opposed to using the preferred method of calling referenceSequence.getHtsPath()). Note
+        // that if the URI scheme for the reference is something other than "file", the REFERENCE_SEQUENCE
+        // object created by this code path won't be valid - but we still have to set it here in case
+        // the tool tries to access REFERENCE_SEQUENCE directly (such tools will subsequently fail given
+        // a non-local file anyway, but this prevents them from immediately throwing an NPE).
+        final PicardHtsPath refHtsPath = referenceSequence.getHtsPath();
+        REFERENCE_SEQUENCE = ReferenceArgumentCollection.getFileSafe(refHtsPath, Log.getInstance(this.getClass()));
 
         // The TMP_DIR setting section below was moved from instanceMain() to here due to timing issues
         // related to checking whether R is installed. Certain programs, such as CollectInsertSizeMetrics

src/main/java/picard/cmdline/argumentcollections/OptionalReferenceArgumentCollection.java

@@ -25,24 +25,33 @@
 package picard.cmdline.argumentcollections;
 
 import htsjdk.samtools.Defaults;
+import htsjdk.samtools.util.Log;
 import org.broadinstitute.barclay.argparser.Argument;
 import picard.cmdline.StandardOptionDefinitions;
+import picard.nio.PicardHtsPath;
 
 import java.io.File;
+import java.nio.file.Path;
 
 /**
  * Picard default argument collection for an optional reference.
  */
 public class OptionalReferenceArgumentCollection implements ReferenceArgumentCollection {
+    private final static Log log = Log.getInstance(OptionalReferenceArgumentCollection.class);
 
     @Argument(shortName = StandardOptionDefinitions.REFERENCE_SHORT_NAME, doc = "Reference sequence file.", common = true, optional = true)
-    public File REFERENCE_SEQUENCE = Defaults.REFERENCE_FASTA;
+    public PicardHtsPath REFERENCE_SEQUENCE = Defaults.REFERENCE_FASTA == null ? null : new PicardHtsPath(Defaults.REFERENCE_FASTA.getAbsolutePath());
 
-    /**
-     * @return The reference provided by the user, if any, or the default defined by {@code htsjdk.samtools.Defaults.REFERENCE_FASTA}
-     */
     @Override
     public File getReferenceFile() {
+        return ReferenceArgumentCollection.getFileSafe(REFERENCE_SEQUENCE, log);
+    }
+
+    @Override
+    public Path getReferencePath() { return REFERENCE_SEQUENCE == null ? null: REFERENCE_SEQUENCE.toPath(); }
+
+    @Override
+    public PicardHtsPath getHtsPath() {
         return REFERENCE_SEQUENCE;
-    };
+    }
 }

src/main/java/picard/cmdline/argumentcollections/ReferenceArgumentCollection.java

@@ -25,13 +25,68 @@
 package picard.cmdline.argumentcollections;
 
 import java.io.File;
+import java.nio.file.Path;
+
+import htsjdk.samtools.util.Log;
+import picard.nio.PicardBucketUtils;
+import picard.nio.PicardHtsPath;
 
 /**
  * Base interface for a reference argument collection.
  */
 public interface ReferenceArgumentCollection {
     /**
-     * @return The reference provided by the user, if any, or the default, if any.
+     * This method is retained for backward compatibility with legacy tools that have not been updated to support PicardHtsPath input files.
+     * The preferred methods for accessing the reference file provided on the command line is either getHtsPath() or getReferencePath().
+     *
+     * TODO: update tools that call this method to use getHtsPath()
+     *
+     * @return The reference provided by the user, or the default defined by {@code htsjdk.samtools.Defaults.REFERENCE_FASTA}. May be null.
      */
     File getReferenceFile();
+
+    /**
+     * This method first checks if the PicardHtsPath is null, thereby avoiding NPE that results from getHtsPath.toPath().
+     * Use this for providing input to methods that expect the Path to be null when the reference is absent e.g. SamReaderFactory.referenceSequence().
+     *
+     * @return The reference provided by the user or the default as an nio Path. May be null.
+     */
+    default Path getReferencePath(){
+        return getHtsPath() == null ? null : getHtsPath().toPath();
+    }
+
+    /**
+     *  Returns a PicardHtsPath for the reference input. Maybe be null. Implementers of this interface should override with an appropriate implementation.
+     * This currently does not support remote paths set via HtsJdk.Defaults.REFERENCE_FASTA, since that uses a `File` object.
+     *
+     * @return The reference provided by the user, if any, or the default, if any, as a PicardHtsPath. May be null.
+     */
+    default PicardHtsPath getHtsPath(){
+        return getReferenceFile() == null ? null : new PicardHtsPath(getReferenceFile());
+    }
+
+    /**
+     * @return A "safe" File object for any reference path.
+     *
+     * For files that reside on a local file system, this returns a valid File object. Files that reside on
+     * a non-local file system can't be accessed via a File object, so return a placeholder File object that
+     * will defer failure until the File object is actually accessed. This allows code paths that blindly propagate
+     * the value returned by calls to getReferenceFile to not get an NPE, and to fail gracefully downstream
+     * with an error message that includes the reference file specifier.
+     */
+    static File getFileSafe(final PicardHtsPath picardPath, final Log log) {
+        if (picardPath == null) {
+            return null;
+        } else if (picardPath.getScheme().equals(PicardBucketUtils.FILE_SCHEME)) {
+            // file on a local file system
+            return picardPath.toPath().toFile();
+        } else {
+            log.warn(String.format(
+                    "The reference specified by %s cannot be used as a local file object",
+                    picardPath.getRawInputString()));
+            // toPath().toFile() would throw here, so use the File constructor to create a placeholder
+            // object and defer failure until downstream code attempts to actually use the File object
+            return new File(picardPath.getRawInputString());
+        }
+    }
 }

src/main/java/picard/cmdline/argumentcollections/RequiredReferenceArgumentCollection.java

@@ -24,23 +24,31 @@
 
 package picard.cmdline.argumentcollections;
 
+import htsjdk.samtools.util.Log;
 import org.broadinstitute.barclay.argparser.Argument;
 import picard.cmdline.StandardOptionDefinitions;
+import picard.nio.PicardHtsPath;
 
 import java.io.File;
+import java.nio.file.Path;
 
 /**
  * Argument collection for references that are required (and not common).
  */
 public class RequiredReferenceArgumentCollection implements ReferenceArgumentCollection {
+    private final static Log log = Log.getInstance(RequiredReferenceArgumentCollection.class);
 
-    @Argument(shortName = StandardOptionDefinitions.REFERENCE_SHORT_NAME, doc = "Reference sequence file.", common = false)
-    public File REFERENCE_SEQUENCE;
+    @Argument(shortName = StandardOptionDefinitions.REFERENCE_SHORT_NAME, doc = "Reference sequence file.")
+    public PicardHtsPath REFERENCE_SEQUENCE;
 
-    /**
-     * @return The reference provided by the user.
-     */
     public File getReferenceFile() {
-        return REFERENCE_SEQUENCE;
-    };
+        return ReferenceArgumentCollection.getFileSafe(REFERENCE_SEQUENCE, log);
+    }
+
+    @Override
+    public Path getReferencePath() { return REFERENCE_SEQUENCE == null ? null: REFERENCE_SEQUENCE.toPath(); }
+
+    @Override
+    public PicardHtsPath getHtsPath() { return REFERENCE_SEQUENCE; }
+
 }

src/main/java/picard/nio/DeleteRecursive.java

@@ -9,7 +9,7 @@
 
 /**
  *
- * Copied from GATK; to be removed once the original GATK code is ported to htsjdk
+ * Adapted from GATK.
  *
  * Class to hold a set of {@link Path} to be delete on the JVM exit through a shutdown hook.
  *
@@ -58,7 +58,7 @@ static void runHooks() {
         Collections.reverse(toBeDeleted);
         for (Path path : toBeDeleted) {
             try {
-                GATKIOUtils.deleteRecursively(path);
+                PicardIOUtils.deleteRecursively(path);
             } catch (final Exception e) {
                 // do nothing if itcannot be deleted, because it is a shutdown hook
                 LOG.debug(e, "Could not recursively delete ", path.toString(), " during JVM shutdown because we encountered the following exception:");