More tests and javadoc.

src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineProgram.java

@@ -156,7 +156,7 @@ public Object instanceMainPostParseArgs() {
             tmpDir = new GATKPath(System.getProperty("java.io.tmpdir"));
         }
 
-        // Build the default headers
+        // Build the defauNlt headers
         final ZonedDateTime startDateTime = ZonedDateTime.now();
         this.defaultHeaders.add(new StringHeader(commandLine));
         this.defaultHeaders.add(new StringHeader("Started on: " + Utils.getDateTimeForDisplay(startDateTime)));

src/test/java/org/broadinstitute/hellbender/engine/BundleSupportIntegrationTest.java

@@ -0,0 +1,34 @@
+package org.broadinstitute.hellbender.engine;
+
+import htsjdk.beta.io.IOPathUtils;
+import htsjdk.beta.io.bundle.Bundle;
+import htsjdk.beta.io.bundle.BundleJSON;
+import htsjdk.io.IOPath;
+import org.broadinstitute.hellbender.GATKBaseTest;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.IOException;
+
+public class BundleSupportIntegrationTest extends GATKBaseTest {
+
+    // this test uses a serialized bundle file to ensure that we don't unintentionally pick up any
+    // code (like, from htsjdk) that introduces backward compatibility issues
+    @Test
+    public void testReadWriteSerializedReferenceBundle() throws IOException {
+        // This test file contains absolute paths to files on a local dev machine, so it shouldn't really be used
+        // for anything other than this test, since the absolute paths are unlikely to work on any other machine.
+        // But here we just want to make sure we can consume and roundtrip it without error
+        final IOPath testBundleFilePath = new GATKPath("src/test/resources/org/broadinstitute/hellbender/engine/print_reads_bundle_do_not_use.json");
+
+        // get our test bundle from the file (ensure we canparse it), then write it out to a temp file, read it back
+        // in, and compare
+        final Bundle testBundle = BundleJSON.toBundle(IOPathUtils.getStringFromPath(testBundleFilePath));
+        final IOPath roundTrippedBundleFilePath = new GATKPath(
+                createTempPath("testReadWriteSerializedReferenceBundle", ".json").toString());
+        IOPathUtils.writeStringToPath(roundTrippedBundleFilePath, BundleJSON.toJSON(testBundle));
+        final Bundle roundTrippedBundle = BundleJSON.toBundle(IOPathUtils.getStringFromPath(testBundleFilePath));
+        Assert.assertTrue(Bundle.equalsIgnoreOrder(roundTrippedBundle, testBundle));
+    }
+
+}

src/test/java/org/broadinstitute/hellbender/engine/MultiVariantWalkerIntegrationTest.java

@@ -167,8 +167,7 @@ private static IOPath createRemoteBundleForFile(
             final File index1,
             final File vcf2,
             final File index2) throws IOException {
-        //TODO: replace this path with getGCPTestStaging()
-        final String remotePath = BucketUtils.randomRemotePath("gs://hellbender/test/staging/remoteBundles", "remote_bundle_test", "dir");
+        final String remotePath = BucketUtils.randomRemotePath(getGCPTestStaging() + "remoteBundles", "remote_bundle_test", "dir");
         final Path remoteDirPath = IOUtils.getPath(remotePath + "/");
 
         Files.createDirectory(remoteDirPath);

src/test/java/org/broadinstitute/hellbender/tools/CreateBundleIntegrationTest.java

@@ -3,6 +3,7 @@
 import htsjdk.beta.io.bundle.*;
 import htsjdk.beta.plugin.IOUtils;
 import htsjdk.beta.plugin.variants.VariantsBundle;
+import org.broadinstitute.barclay.argparser.CommandLineException;
 import org.broadinstitute.hellbender.CommandLineProgramTest;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.engine.GATKPath;
@@ -13,24 +14,28 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.stream.Collectors;
 
 public class CreateBundleIntegrationTest extends CommandLineProgramTest {
 
     // force our local paths to use absolute path names to make BundleResource and IOPath equality checks easier,
     // since once a bundle is round-tripped/serialized to JSON, the resources will always contain absolute path names
     // for local files
+
+    //NOTE: These variables are Strings, but they are initialized to Strings obtained by first creating a GATKPath,
+    // and then calling getURIString on the resulting object. This is just  shortcut to normalize them so they
+    // match the strings that will be embedded in the bundles created by the CreateBundle tool (i.e., to have
+    // full/absolute paths and protocol schemes).
     private final static String LOCAL_VCF = new GATKPath(getTestDataDir() + "/count_variants_withSequenceDict.vcf").getURIString();
     private final static String LOCAL_VCF_IDX = new GATKPath(getTestDataDir() + "/count_variants_withSequenceDict.vcf.idx").getURIString();
     private final static String LOCAL_VCF_GZIP = new GATKPath("src/test/resources/large/NA24385.vcf.gz").getURIString();
     private final static String LOCAL_VCF_TBI = new GATKPath("src/test/resources/large/NA24385.vcf.gz.tbi").getURIString();
     private final static String LOCAL_VCF_WITH_NO_INDEX = new GATKPath("src/test/resources/org/broadinstitute/hellbender/tools/count_variants_withSequenceDict_noIndex.vcf").getURIString();
-    private final static String CLOUD_VCF = "gs://hellbender/test/resources/large/1000G.phase3.broad.withGenotypes.chr20.10100000.vcf";
-    private final static String CLOUD_VCF_IDX = "gs://hellbender/test/resources/large/1000G.phase3.broad.withGenotypes.chr20.10100000.vcf.idx";
+    private final static String CLOUD_VCF = GCS_GATK_TEST_RESOURCES + "large/1000G.phase3.broad.withGenotypes.chr20.10100000.vcf";
+    private final static String CLOUD_VCF_IDX = GCS_GATK_TEST_RESOURCES + "large/1000G.phase3.broad.withGenotypes.chr20.10100000.vcf.idx";
 
-    private final static String LOCAL_FASTA = "src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta";
-    private final static String LOCAL_FASTA_INDEX = "src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta.fai";
-    private final static String LOCAL_FASTA_DICT = "src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta.dict";
+    private final static String LOCAL_FASTA = new GATKPath("src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta").getURIString();
+    private final static String LOCAL_FASTA_INDEX = new GATKPath("src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta.fai").getURIString();
+    private final static String LOCAL_FASTA_DICT = new GATKPath("src/test/resources/large/Homo_sapiens_assembly38.20.21.dict").getURIString();
 
     private final static String CUSTOM_PRIMARY_CT = "primary_ct";
     private final static String CUSTOM_SECONDARY_CT = "secondary_ct";
@@ -41,22 +46,21 @@ public Object[][] bundleCases() {
         return new Object[][] {
                 // primary, primary tag, secondary, secondary tag, other(s), other tag(s), suppressResourceResolution, expectedBundle
 
-                // VCF bundle cases, with AUTOMATIC secondary resolution, and INFERRED content types
+                // VCF bundle cases, with AUTOMATIC secondary resolution, and INFERRED primary content types
                 {LOCAL_VCF, null, null, null, null, null, false, new VariantsBundle(new GATKPath(LOCAL_VCF), new GATKPath(LOCAL_VCF_IDX))},
-                {LOCAL_VCF, null, LOCAL_VCF_IDX, null, null, null, false, new VariantsBundle(new GATKPath(LOCAL_VCF), new GATKPath(LOCAL_VCF_IDX))},
+                {LOCAL_VCF, null, LOCAL_VCF_IDX, BundleResourceType.CT_VARIANTS_INDEX, null, null, false, new VariantsBundle(new GATKPath(LOCAL_VCF), new GATKPath(LOCAL_VCF_IDX))},
                 {LOCAL_VCF_GZIP, null, null, null, null, null, false, new VariantsBundle(new GATKPath(LOCAL_VCF_GZIP), new GATKPath(LOCAL_VCF_TBI))},
+                {LOCAL_VCF_GZIP, null, LOCAL_VCF_TBI, BundleResourceType.CT_VARIANTS_INDEX, null, null, true, new VariantsBundle(new GATKPath(LOCAL_VCF_GZIP), new GATKPath(LOCAL_VCF_TBI))},
                 {CLOUD_VCF, null, null, null, null, null, false, new VariantsBundle(new GATKPath(CLOUD_VCF), new GATKPath(CLOUD_VCF_IDX))},
-                {CLOUD_VCF, null, CLOUD_VCF_IDX, null, null, null, false, new VariantsBundle(new GATKPath(CLOUD_VCF), new GATKPath(CLOUD_VCF_IDX))},
+                {CLOUD_VCF, null, CLOUD_VCF_IDX, BundleResourceType.CT_VARIANTS_INDEX, null, null, false, new VariantsBundle(new GATKPath(CLOUD_VCF), new GATKPath(CLOUD_VCF_IDX))},
 
-                // VCF bundle cases, with SUPPRESSED secondary resolution, and INFERRED content types
+                // VCF bundle cases, with SUPPRESSED secondary resolution, and INFERRED primary content types
                 {LOCAL_VCF, null, null, null, null, null, true, new VariantsBundle(new GATKPath(LOCAL_VCF))},
-                {LOCAL_VCF, null, LOCAL_VCF_IDX, null, null, null, true, new VariantsBundle(new GATKPath(LOCAL_VCF), new GATKPath(LOCAL_VCF_IDX))},
+                // local vcf that has no index, but since suppressSecondaryResourceResolution is true, we don't throw since we don't try to infer the index
                 {LOCAL_VCF_WITH_NO_INDEX, null, null, null, null, null, true, new VariantsBundle(new GATKPath(LOCAL_VCF_WITH_NO_INDEX))},
-                {LOCAL_VCF_GZIP, null, LOCAL_VCF_TBI, null, null, null, true, new VariantsBundle(new GATKPath(LOCAL_VCF_GZIP), new GATKPath(LOCAL_VCF_TBI))},
                 {CLOUD_VCF, null, null, null, null, null, true, new VariantsBundle(new GATKPath(CLOUD_VCF))},
-                {CLOUD_VCF, null, CLOUD_VCF_IDX, null, null, null, true, new VariantsBundle(new GATKPath(CLOUD_VCF), new GATKPath(CLOUD_VCF_IDX))},
 
-                // VCF bundle cases, with AUTOMATIC secondary resolution, and EXPLICIT content types
+                // VCF bundle cases, with AUTOMATIC secondary resolution, and EXPLICIT primary content types
                 {LOCAL_VCF, BundleResourceType.CT_VARIANT_CONTEXTS, null, null, null, null, false, new VariantsBundle(new GATKPath(LOCAL_VCF), new GATKPath(LOCAL_VCF_IDX))},
                 {LOCAL_VCF, BundleResourceType.CT_VARIANT_CONTEXTS, LOCAL_VCF_IDX, BundleResourceType.CT_VARIANTS_INDEX, null, null, false, new VariantsBundle(new GATKPath(LOCAL_VCF), new GATKPath(LOCAL_VCF_IDX))},
 
@@ -70,9 +74,24 @@ public Object[][] bundleCases() {
                         .addPrimary(new IOPathResource(new GATKPath(LOCAL_VCF), BundleResourceType.CT_VARIANT_CONTEXTS))
                         .addSecondary(new IOPathResource(new GATKPath(LOCAL_VCF_IDX), BundleResourceType.CT_VARIANTS_INDEX))
                         .addSecondary(new IOPathResource(new GATKPath(new GATKPath("someVariantsCompanion.txt").getURIString()), "someVariantsCT"))
-                        .build()},
+                        .build()
+                },
 
                 // reference bundles
+                { LOCAL_FASTA, null, null, null, null, null, false,
+                        new BundleBuilder()
+                                .addPrimary(new IOPathResource(new GATKPath(LOCAL_FASTA), BundleResourceType.CT_HAPLOID_REFERENCE))
+                                .addSecondary(new IOPathResource(new GATKPath(LOCAL_FASTA_INDEX), BundleResourceType.CT_REFERENCE_INDEX))
+                                .addSecondary(new IOPathResource(new GATKPath(LOCAL_FASTA_DICT), BundleResourceType.CT_REFERENCE_DICTIONARY))
+                                .build()
+                },
+                { LOCAL_FASTA, BundleResourceType.CT_HAPLOID_REFERENCE, LOCAL_FASTA_INDEX, BundleResourceType.CT_REFERENCE_INDEX, Arrays.asList(LOCAL_FASTA_DICT), Arrays.asList(BundleResourceType.CT_REFERENCE_DICTIONARY), false,
+                        new BundleBuilder()
+                                .addPrimary(new IOPathResource(new GATKPath(LOCAL_FASTA), BundleResourceType.CT_HAPLOID_REFERENCE))
+                                .addSecondary(new IOPathResource(new GATKPath(LOCAL_FASTA_INDEX), BundleResourceType.CT_REFERENCE_INDEX))
+                                .addSecondary(new IOPathResource(new GATKPath(LOCAL_FASTA_DICT), BundleResourceType.CT_REFERENCE_DICTIONARY))
+                                .build()
+                },
 
                 // "custom" bundles
                 {
@@ -105,17 +124,26 @@ public Object[][] negativeBundleCases() {
         return new Object[][] {
                 // primary, primary tag, secondary, secondary tag, other(s), other tag(s), suppressIndexResolution, expectedBundle
 
-                // no index file can be inferred
+                // no vcf index file can be inferred
                 {LOCAL_VCF_WITH_NO_INDEX, null, null, null, null, null, false, new VariantsBundle(new GATKPath(LOCAL_VCF_WITH_NO_INDEX))},
+                // vcf bundle with secondary/other content type not explicitly provided
+                {LOCAL_VCF, BundleResourceType.CT_VARIANT_CONTEXTS, null, null, Arrays.asList("other.txt"), null, false, null},
+                {LOCAL_VCF, null, LOCAL_VCF_IDX, null, null, null, false, new VariantsBundle(new GATKPath(LOCAL_VCF), new GATKPath(LOCAL_VCF_IDX))},
+                {LOCAL_VCF, null, LOCAL_VCF_IDX, null, null, null, true, new VariantsBundle(new GATKPath(LOCAL_VCF), new GATKPath(LOCAL_VCF_IDX))},
+                {LOCAL_VCF_GZIP, null, LOCAL_VCF_TBI, null, null, null, true, new VariantsBundle(new GATKPath(LOCAL_VCF_GZIP), new GATKPath(LOCAL_VCF_TBI))},
+                {CLOUD_VCF, null, CLOUD_VCF_IDX, null, null, null, false, new VariantsBundle(new GATKPath(CLOUD_VCF), new GATKPath(CLOUD_VCF_IDX))},
+                {CLOUD_VCF, null, CLOUD_VCF_IDX, null, null, null, true, new VariantsBundle(new GATKPath(CLOUD_VCF), new GATKPath(CLOUD_VCF_IDX))},
                 // primary content type not provided, and cannot be inferred from the extension
                 {"primaryFile.ext", null, null, null, null, null, false, null},
                 // secondary content type not provided
                 {"primaryFile.ext", CUSTOM_PRIMARY_CT, "secondaryFile.ext", null, null, null, false, null},
 
+                // reference input with unknown content type specified
+                { LOCAL_FASTA, null, LOCAL_FASTA_INDEX, "unknown", null, null, false, null},
+
                 // other bundle with other content type not provided
                 {"primaryFile.ext", CUSTOM_PRIMARY_CT, "secondaryFile.ext", CUSTOM_SECONDARY_CT, Arrays.asList("other.txt"), null, false, null},
-                // vcf bundle with other content type not provided
-                {LOCAL_VCF, BundleResourceType.CT_VARIANT_CONTEXTS, null, null, Arrays.asList("other.txt"), null, false, null},
+
         };
     }
 
@@ -145,6 +173,17 @@ public void testNegativeBundleCases(
         doCreateBundleTest (primaryInput, primaryInputTag, secondaryInput, secondaryInputTag, otherInputs, otherInputTags, suppressResourceResolution, expectedBundle);
     }
 
+    @Test(expectedExceptions={CommandLineException.class})
+    public void testRequireBundleExtension() {
+        final GATKPath outputPath = new GATKPath(createTempFile("test", ".bundle.BOGUS").getAbsolutePath().toString());
+        final List<String> args = new ArrayList<>();
+        args.add("--" + StandardArgumentDefinitions.PRIMARY_RESOURCE_LONG_NAME);
+        args.add(LOCAL_FASTA);
+        args.add("--" + StandardArgumentDefinitions.OUTPUT_LONG_NAME);
+        args.add(outputPath.toString());
+        runCommandLine(args);
+    }
+
     private void doCreateBundleTest(
             final String primaryInput,
             final String primaryInputTag,
@@ -176,10 +215,6 @@ private void doCreateBundleTest(
         args.add("--" + StandardArgumentDefinitions.OUTPUT_LONG_NAME);
         args.add(outputPath.toString());
 
-        System.out.println();
-        System.out.println(args.stream().collect(Collectors.joining("\n ")));
-        System.out.println();
-
         runCommandLine(args);
 
         final Bundle actualBundle = BundleJSON.toBundle(IOUtils.getStringFromPath(outputPath), GATKPath::new);

src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java

@@ -1,22 +1,29 @@
 package org.broadinstitute.hellbender.tools;
 
-import htsjdk.samtools.SamReaderFactory;
-import htsjdk.samtools.ValidationStringency;
+import htsjdk.beta.io.IOPathUtils;
+import htsjdk.beta.io.bundle.*;
+import htsjdk.io.IOPath;
+import htsjdk.samtools.*;
+import htsjdk.samtools.cram.ref.ReferenceSource;
 import org.broadinstitute.hellbender.GATKBaseTest;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.engine.GATKPath;
 import org.broadinstitute.hellbender.engine.ReadsDataSource;
 import org.broadinstitute.hellbender.engine.ReadsPathDataSource;
 import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
 import org.broadinstitute.hellbender.testutils.SamAssertionUtils;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.gcs.BucketUtils;
+import org.broadinstitute.hellbender.utils.io.IOUtils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.Arrays;
 import java.util.List;
 
@@ -104,4 +111,50 @@ public void testHttpPaths(String reads, String index, String nonHttpReads, Strin
         SamAssertionUtils.assertEqualBamFiles(out, out2, false, ValidationStringency.DEFAULT_STRINGENCY);
     }
 
+    @Test(groups = {"cloud"})
+    public void testPrintReadsWithReferenceBundle() throws IOException {
+        // test that both reading and writing a cram work when the reference is specified via a bundle where the
+        // reference, reference index, and reference dictionary are all in different buckets
+        final IOPath testFastaFile = new GATKPath(getTestDataDir() + "/print_reads.fasta");
+        final IOPath testIndexFile = new GATKPath(getTestDataDir() + "/print_reads.fasta.fai");
+        final IOPath testDictFile = new GATKPath(getTestDataDir() + "/print_reads.dict");
+
+        final String targetBucketName = BucketUtils.randomRemotePath(getGCPTestStaging(), "testPrintReadsWithReferenceBundle", "") + "/";
+        final IOPath targetBucket = new GATKPath(targetBucketName);
+        IOUtils.deleteOnExit(targetBucket.toPath());
+
+        final Path remoteFasta = Files.copy(testFastaFile.toPath(), new GATKPath(targetBucketName + "print_reads.fasta").toPath());
+        final IOPath targetIndex = new GATKPath(targetBucketName + "refindex/print_reads.fasta.fai");
+        final Path remoteFastaIndex = Files.copy(testIndexFile.toPath(), targetIndex.toPath());
+        final IOPath targetDict = new GATKPath(targetBucketName + "refdict/print_reads.dict");
+        final Path remoteFastaDict = Files.copy(testDictFile.toPath(), targetDict.toPath());
+
+        // create a bundle with the remote reference, index, and dict files
+        final Bundle refBundle = new BundleBuilder()
+                .addPrimary(new IOPathResource(new GATKPath(remoteFasta.toUri().toString()), BundleResourceType.CT_HAPLOID_REFERENCE))
+                .addSecondary(new IOPathResource(new GATKPath(remoteFastaIndex.toUri().toString()), BundleResourceType.CT_REFERENCE_INDEX))
+                .addSecondary(new IOPathResource(new GATKPath(remoteFastaDict.toUri().toString()), BundleResourceType.CT_REFERENCE_DICTIONARY))
+                .build();
+        final IOPath bundleFilePath = new GATKPath(targetBucketName + "refBundle.json");
+        IOPathUtils.writeStringToPath(bundleFilePath, BundleJSON.toJSON(refBundle));
+
+        final IOPath targetOutCRAM = new GATKPath(IOUtils.createTempFile("testReferenceSequenceForNioBundle", ".cram").getAbsolutePath());
+        final ArgumentsBuilder args = new ArgumentsBuilder()
+                .addInput(getTestDataDir() + "/print_reads.cram")
+                .addReference(bundleFilePath.toString())
+                .addOutput(targetOutCRAM.toString());
+                runCommandLine(args);
+
+        int count = 0;
+        try (final SamReader in = SamReaderFactory.makeDefault()
+                .validationStringency(ValidationStringency.SILENT)
+                .referenceSource(new ReferenceSource(bundleFilePath.toPath()))
+                .open(targetOutCRAM.toPath())) {
+            for (@SuppressWarnings("unused") final SAMRecord rec : in) {
+                count++;
+            }
+        }
+        Assert.assertEquals(count, 8);
+    }
+
 }