clean up

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

@@ -25,6 +25,7 @@
 
 import com.intel.gkl.compression.IntelDeflaterFactory;
 import com.intel.gkl.compression.IntelInflaterFactory;
+import htsjdk.io.IOPath;
 import htsjdk.samtools.Defaults;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileWriterFactory;
@@ -341,7 +342,7 @@ protected boolean parseArgs(final String[] argv) {
         // 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();
+        final IOPath 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

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

@@ -27,6 +27,7 @@
 import java.io.File;
 import java.nio.file.Path;
 
+import htsjdk.io.IOPath;
 import htsjdk.samtools.util.Log;
 import picard.nio.PicardBucketUtils;
 import picard.nio.PicardHtsPath;
@@ -61,7 +62,7 @@ default Path getReferencePath(){
      *
      * @return The reference provided by the user, if any, or the default, if any, as a PicardHtsPath. May be null.
      */
-    default PicardHtsPath getHtsPath(){
+    default IOPath getHtsPath(){
         return getReferenceFile() == null ? null : new PicardHtsPath(getReferenceFile());
     }
 
@@ -74,7 +75,7 @@ default PicardHtsPath getHtsPath(){
      * 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) {
+    static File getFileSafe(final IOPath picardPath, final Log log) {
         if (picardPath == null) {
             return null;
         } else if (picardPath.getScheme().equals(PicardBucketUtils.FILE_SCHEME)) {

src/main/java/picard/nio/PicardBucketUtils.java

@@ -1,16 +1,12 @@
 package picard.nio;
 
-import com.google.cloud.storage.contrib.nio.CloudStorageFileSystem;
-import com.google.cloud.storage.contrib.nio.CloudStoragePath;
-import htsjdk.io.HtsPath;
 import htsjdk.io.IOPath;
 import htsjdk.samtools.util.FileExtensions;
 import htsjdk.utils.ValidationUtils;
 import picard.PicardException;
 
 import java.util.UUID;
 
-
 /**
  * Derived from BucketUtils.java in GATK
  */
@@ -143,6 +139,9 @@ public static boolean isLocalPath(final IOPath path){
     }
 
     /**
+     * As of August 2024, we only support Google Cloud.
+     * Will add other filesystems (e.g. Azure, AWS) when ready.
+     *
      * @return whether the cloud filesystem is currently supported by Picard.
      */
     public static boolean isSupportedCloudFilesystem(final IOPath path){

src/test/java/picard/cmdline/CommandLineProgramTest.java

@@ -1,5 +1,6 @@
 package picard.cmdline;
 
+import htsjdk.io.IOPath;
 import org.apache.commons.io.FileUtils;
 import org.testng.annotations.AfterClass;
 import picard.PicardException;
@@ -24,13 +25,13 @@ public abstract class CommandLineProgramTest {
     public static final File CHR_M_DICT = new File(REFERENCE_TEST_DIR,"chrM.reference.dict");
 
     // These are the hg19 references with chromosome names "1" (rather than "chr1")
-    public static final PicardHtsPath HG19_CHR2021_GCLOUD = PicardHtsPath.resolve(GCloudTestUtils.getTestInputPath(), "picard/references/human_g1k_v37.20.21.fasta");
-    public static final PicardHtsPath HG19_CHR2021 = new PicardHtsPath("testdata/picard/reference/human_g1k_v37.20.21.fasta.gz");
+    public static final IOPath HG19_CHR2021_GCLOUD = PicardHtsPath.resolve(GCloudTestUtils.getTestInputPath(), "picard/references/human_g1k_v37.20.21.fasta");
+    public static final IOPath HG19_CHR2021 = new PicardHtsPath("testdata/picard/reference/human_g1k_v37.20.21.fasta.gz");
 
-    public static final PicardHtsPath NA12878_MINI_GCLOUD = PicardHtsPath.resolve(GCloudTestUtils.getTestInputPath(), "picard/bam/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n100.bam");
-    public static final PicardHtsPath NA12878_MINI_CRAM_GCLOUD = PicardHtsPath.resolve(GCloudTestUtils.getTestInputPath(), "picard/bam/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n100.cram");
-    public static final PicardHtsPath NA12878_MEDIUM_GCLOUD = PicardHtsPath.resolve(GCloudTestUtils.getTestInputPath(), "picard/bam/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n10000.bam");
-    public static final PicardHtsPath NA12878_MEDIUM_CRAM_GCLOUD = PicardHtsPath.resolve(GCloudTestUtils.getTestInputPath(), "picard/bam/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n10000.cram");
+    public static final IOPath NA12878_MINI_GCLOUD = PicardHtsPath.resolve(GCloudTestUtils.getTestInputPath(), "picard/bam/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n100.bam");
+    public static final IOPath NA12878_MINI_CRAM_GCLOUD = PicardHtsPath.resolve(GCloudTestUtils.getTestInputPath(), "picard/bam/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n100.cram");
+    public static final IOPath NA12878_MEDIUM_GCLOUD = PicardHtsPath.resolve(GCloudTestUtils.getTestInputPath(), "picard/bam/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n10000.bam");
+    public static final IOPath NA12878_MEDIUM_CRAM_GCLOUD = PicardHtsPath.resolve(GCloudTestUtils.getTestInputPath(), "picard/bam/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n10000.cram");
 
     // A per-test-class directory that will be deleted after the tests are complete.
     private File tempOutputDir;

src/test/java/picard/nio/PicardBucketUtilsTest.java

@@ -1,16 +1,11 @@
 package picard.nio;
 
-import htsjdk.io.HtsPath;
 import htsjdk.io.IOPath;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 import picard.util.GCloudTestUtils;
 
-import java.net.URI;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-
 public class PicardBucketUtilsTest {
 
     @DataProvider(name="testGetTempFilePathDataProvider")
@@ -38,9 +33,9 @@ public void testGetTempFilePath(final IOPath directory, final String prefix, fin
     @DataProvider
     public Object[][] getVariousPathsForPrefetching(){
         return new Object[][]{
-                {new HtsPath("file:///local/file"), false},
-                {new HtsPath("gs://abucket/bucket"), true},
-                {new HtsPath("gs://abucket_with_underscores"), true},
+                {new PicardHtsPath("file:///local/file"), false},
+                {new PicardHtsPath("gs://abucket/bucket"), true},
+                {new PicardHtsPath("gs://abucket_with_underscores"), true},
         };
     }
 

src/test/java/picard/sam/RevertSamTest.java

@@ -618,7 +618,7 @@ public Object[][] getCloudTestData() {
                 // Output by read group using the output map, write output bams in the cloud
                 {NA12878_MEDIUM_GCLOUD, null, OUTPUT_BY_READ_GROUP, DEFAULT_CLOUD_TEST_OUTPUT_DIR, null },
                 // Output by read group using the local output map, write output bams in the cloud
-                {NA12878_MEDIUM_GCLOUD, null, OUTPUT_BY_READ_GROUP, new PicardHtsPath(REVERT_SAM_LOCAL_TEST_DATA_DIR), null }, // tsato: relative local dir...just wrap it in PicardHtsPath to see what happens
+                {NA12878_MEDIUM_GCLOUD, null, OUTPUT_BY_READ_GROUP, new PicardHtsPath(REVERT_SAM_LOCAL_TEST_DATA_DIR), null },
                 // Cram input, output a CRAM for each read group
                 {NA12878_MEDIUM_CRAM_GCLOUD, null, OUTPUT_BY_READ_GROUP, DEFAULT_CLOUD_TEST_OUTPUT_DIR, HG19_CHR2021 },
                 // Cram input in the cloud, single cloud cram output