Cloud-enable BuildBamIndex outputs.

src/main/java/picard/sam/BuildBamIndex.java

@@ -75,7 +75,7 @@ public class BuildBamIndex extends CommandLineProgram {
     @Argument(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME,
             doc = "The BAM index file. Defaults to x.bai if INPUT is x.bam, otherwise INPUT.bai.\n" +
                     "If INPUT is a URL and OUTPUT is unspecified, defaults to a file in the current directory.", optional = true)
-    public File OUTPUT;
+    public PicardHtsPath OUTPUT;
 
     /**
      * Main method for the program.  Checks that all input files are present and
@@ -91,20 +91,17 @@ protected int doWork() {
             final String baseFileName = inputPath.getFileName().toString();
 
             // only BAI indices can be created for now, although CSI indices can be read as well
-            if (baseFileName.endsWith(FileExtensions.BAM)) {
+            if (INPUT.hasExtension(FileExtensions.BAM)) {
 
                 final int index = baseFileName.lastIndexOf('.');
-                OUTPUT = new File(baseFileName.substring(0, index) + FileExtensions.BAI_INDEX);
-
+                final String outputIndexFileName = baseFileName.substring(0, index) + FileExtensions.BAI_INDEX;
+                OUTPUT = new PicardHtsPath(inputPath.resolveSibling(outputIndexFileName).toUri().toString());
             } else {
-                OUTPUT = new File(baseFileName + FileExtensions.BAI_INDEX);
+                OUTPUT = new PicardHtsPath(inputPath.resolveSibling(baseFileName + FileExtensions.BAI_INDEX).toUri().toString());
             }
         }
 
-        IOUtil.assertFileIsWritable(OUTPUT);
         final SamReader bam;
-
-
         bam = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE)
                 .disable(SamReaderFactory.Option.EAGERLY_DECODE)
                 .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS)
@@ -118,7 +115,7 @@ protected int doWork() {
             throw new SAMException("Input bam file must be sorted by coordinate");
         }
 
-        BAMIndexer.createIndex(bam, OUTPUT);
+        BAMIndexer.createIndex(bam, OUTPUT.toPath());
 
         log.info("Successfully wrote bam index file " + OUTPUT);
         CloserUtil.close(bam);

src/test/java/picard/sam/BuildBamIndexTest.java

@@ -1,72 +1,89 @@
 package picard.sam;
 
+import htsjdk.beta.io.IOPathUtils;
+import htsjdk.io.IOPath;
 import htsjdk.samtools.SAMException;
 import org.apache.commons.io.FileUtils;
 import org.testng.Assert;
-import org.testng.annotations.AfterTest;
 import org.testng.annotations.Test;
 import picard.cmdline.CommandLineProgramTest;
 import picard.nio.PicardHtsPath;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
 
 public class BuildBamIndexTest extends CommandLineProgramTest {
 
     private static final File TEST_DATA_DIR = new File("testdata/picard/indices/");
-    private static final PicardHtsPath INPUT_FILE = new PicardHtsPath(new File(TEST_DATA_DIR, "index_test.sam").getPath());
-    private static final File OUTPUT_SORTED_FILE = new File(TEST_DATA_DIR, "index_test_sorted.bam");
-    private static final File OUTPUT_UNSORTED_FILE = new File(TEST_DATA_DIR, "/index_test_unsorted.bam");
-    private static final File OUTPUT_INDEX_FILE = new File(TEST_DATA_DIR, "/index_test.bam.bai");
+    private static final PicardHtsPath INPUT_UNSORTED_SAM = new PicardHtsPath(new File(TEST_DATA_DIR, "index_test.sam").getPath());
     private static final File EXPECTED_BAI_FILE = new File(TEST_DATA_DIR, "index_test_b.bam.bai");
 
     public String getCommandLineProgramName() { return BuildBamIndex.class.getSimpleName(); }
 
-
     // Test that the index file for a sorted BAM is created
     @Test
     public void testBuildBamIndexOK() throws IOException {
+        final IOPath sortedBAM = IOPathUtils.createTempPath("index_test_sorted", ".bam");
+        // don't create the output index file, but mark it for deletion
+        final Path indexOutput = sortedBAM.toPath().resolveSibling("index_test.bam.bai");
+        indexOutput.toFile().deleteOnExit();
+
+        /* First sort, before indexing */
+        new SortSam().instanceMain(new String[]{
+                "I=" + INPUT_UNSORTED_SAM,
+                "O=" + sortedBAM,
+                "SORT_ORDER=coordinate"});
+
         final List<String> args = new ArrayList<>();
+        args.add("INPUT=" + sortedBAM);
+        args.add("OUTPUT=" + indexOutput);
+        runPicardCommandLine(args);
+        Assert.assertEquals(FileUtils.readFileToByteArray(indexOutput.toFile()), FileUtils.readFileToByteArray(EXPECTED_BAI_FILE));
+    }
+
+    // Test that the index file for a sorted BAM is created in the right place if no output file is specified
+    @Test
+    public void testBuildBamIndexDefaultOutput() throws IOException {
+        final IOPath sortedBAM = IOPathUtils.createTempPath("index_test_sorted", ".bam");
         /* First sort, before indexing */
         new SortSam().instanceMain(new String[]{
-                "I=" + INPUT_FILE,
-                "O=" + OUTPUT_SORTED_FILE,
+                "I=" + INPUT_UNSORTED_SAM,
+                "O=" + sortedBAM,
                 "SORT_ORDER=coordinate"});
 
-        args.add("INPUT=" + OUTPUT_SORTED_FILE);
-        args.add("OUTPUT=" + OUTPUT_INDEX_FILE);
+        // don't create the output index file, but construct the expected name, and mark it for deletion
+        final String expectedIndexFileName = sortedBAM.getURIString().replace(".bam", ".bai");
+        final IOPath indexOutput = new PicardHtsPath(expectedIndexFileName);
+        indexOutput.toPath().toFile().deleteOnExit();
+
+        final List<String> args = new ArrayList<>();
+        args.add("INPUT=" + sortedBAM);
         runPicardCommandLine(args);
-        Assert.assertEquals(FileUtils.readFileToByteArray(OUTPUT_INDEX_FILE),  FileUtils.readFileToByteArray(EXPECTED_BAI_FILE));
+        Assert.assertEquals(FileUtils.readFileToByteArray(indexOutput.toPath().toFile()),  FileUtils.readFileToByteArray(EXPECTED_BAI_FILE));
     }
 
     // Test that the index creation fails when presented with a SAM file
     @Test(expectedExceptions = SAMException.class)
     public void testBuildSamIndexFail() {
         final List<String> args = new ArrayList<>();
-        args.add("INPUT=" + INPUT_FILE);
-        args.add("OUTPUT=" + OUTPUT_INDEX_FILE);
+        args.add("INPUT=" + INPUT_UNSORTED_SAM);
         runPicardCommandLine(args);
     }
 
     // Test that the index creation fails when presented with an unsorted BAM file
     @Test(expectedExceptions = SAMException.class)
     public void testBuildBamIndexFail() {
-        final List<String> args = new ArrayList<>();
+        final IOPath unsortedBAM = IOPathUtils.createTempPath("index_test_sorted", ".bam");
         new SamFormatConverter().instanceMain(new String[]{
-                "INPUT=" + INPUT_FILE,
-                "OUTPUT=" + OUTPUT_UNSORTED_FILE});
+                "INPUT=" + INPUT_UNSORTED_SAM,
+                "OUTPUT=" + unsortedBAM});
 
-        args.add("INPUT=" + OUTPUT_UNSORTED_FILE);
-        args.add("OUTPUT=" + OUTPUT_INDEX_FILE);
+        final List<String> args = new ArrayList<>();
+        args.add("INPUT=" + unsortedBAM);
         runPicardCommandLine(args);
     }
 
-    @AfterTest
-    public void cleanup() throws IOException {
-        FileUtils.forceDeleteOnExit(OUTPUT_INDEX_FILE);
-        FileUtils.forceDeleteOnExit(OUTPUT_SORTED_FILE);
-        FileUtils.forceDeleteOnExit(OUTPUT_UNSORTED_FILE);
-    }
 }