NIO output support for ApplyBQSR

src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/ApplyBQSR.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.hellbender.tools.walkers.bqsr;
 
+import java.nio.file.Path;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.broadinstitute.barclay.argparser.Argument;
@@ -14,6 +15,7 @@
 import org.broadinstitute.hellbender.transformers.BQSRReadTransformer;
 import org.broadinstitute.hellbender.transformers.ReadTransformer;
 import org.broadinstitute.hellbender.utils.Utils;
+import org.broadinstitute.hellbender.utils.io.IOUtils;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 import org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
@@ -75,7 +77,7 @@ public final class ApplyBQSR extends ReadWalker{
     private static final Logger logger = LogManager.getLogger(ApplyBQSR.class);
 
     @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc="Write output to this file")
-    public File OUTPUT;
+    public String OUTPUT;
 
     /**
      * This argument is required for recalibration of base qualities. The recalibration table is a file produced by
@@ -103,7 +105,7 @@ public ReadTransformer makePostReadFilterTransformer(){
 
     @Override
     public void onTraversalStart() {
-        outputWriter = createSAMWriter(OUTPUT, true);
+        outputWriter = createSAMWriter(IOUtils.getPath(OUTPUT), true);
         Utils.warnOnNonIlluminaReadGroups(getHeaderForReads(), logger);
     }
 

src/main/java/org/broadinstitute/hellbender/utils/Utils.java

@@ -5,6 +5,9 @@
 import com.google.common.primitives.Ints;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.tribble.util.ParsingUtils;
+import java.io.FileNotFoundException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
@@ -524,12 +527,40 @@ public static String calcMD5(final byte[] bytes) {
     /**
      * Calculates the MD5 for the specified file and returns it as a String
      *
+     * Warning: this loads the whole file into memory, so it's not suitable
+     * for large files.
+     *
      * @param file file whose MD5 to calculate
      * @return file's MD5 in String form
      * @throws IOException if the file could not be read
      */
     public static String calculateFileMD5( final File file ) throws IOException{
-        return Utils.calcMD5(FileUtils.readFileToByteArray(file));
+        return calculatePathMD5(file.toPath());
+    }
+
+    /**
+     * Calculates the MD5 for the specified file and returns it as a String
+     *
+     * Warning: this loads the whole file into memory, so it's not suitable
+     * for large files.
+     *
+     * @param path file whose MD5 to calculate
+     * @return file's MD5 in String form
+     * @throws IOException if the file could not be read
+     */
+    public static String calculatePathMD5(final Path path) throws IOException{
+        // This doesn't have as nice error messages as FileUtils, but it's close.
+        String fname = path.toUri().toString();
+        if (!Files.exists(path)) {
+            throw new FileNotFoundException("File '" + fname + "' does not exist");
+        }
+        if (Files.isDirectory(path)) {
+            throw new IOException("File '" + fname + "' exists but is a directory");
+        }
+        if (!Files.isRegularFile(path)) {
+            throw new IOException("File '" + fname + "' exists but is not a regular file");
+        }
+        return Utils.calcMD5(Files.readAllBytes(path));
     }
 
     /**

src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java

@@ -14,10 +14,8 @@
 import htsjdk.samtools.SAMUtils;
 import htsjdk.samtools.SamStreams;
 import htsjdk.samtools.cram.build.CramIO;
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
+import java.io.*;
+import java.nio.file.Files;
 import java.nio.file.OpenOption;
 import java.nio.file.Path;
 import java.util.Arrays;
@@ -1131,19 +1129,31 @@ public static SAMFileWriter createCommonSAMWriterFromFactory(
      * Validate that a file has CRAM contents by checking that it has a valid CRAM file header
      * (no matter what the extension).
      *
-     * @param putativeCRAMFile File to check.
+     * @param putativeCRAMPath File to check.
      * @return true if the file has a valid CRAM file header, otherwise false
      */
-    public static boolean hasCRAMFileContents(final File putativeCRAMFile) {
-        try (final FileInputStream fileStream = new FileInputStream(putativeCRAMFile);
-             final BufferedInputStream bis = new BufferedInputStream(fileStream)) {
-            return SamStreams.isCRAMFile(bis);
+    public static boolean hasCRAMFileContents(final Path putativeCRAMPath) {
+        try (final InputStream fileStream = Files.newInputStream(putativeCRAMPath)) {
+            try (final BufferedInputStream bis = new BufferedInputStream(fileStream)) {
+                return SamStreams.isCRAMFile(bis);
+            }
         }
         catch (IOException e) {
             throw new UserException.CouldNotReadInputFile(e.getMessage());
         }
     }
 
+    /**
+     * Validate that a file has CRAM contents by checking that it has a valid CRAM file header
+     * (no matter what the extension).
+     *
+     * @param putativeCRAMFile File to check.
+     * @return true if the file has a valid CRAM file header, otherwise false
+     */
+    public static boolean hasCRAMFileContents(final File putativeCRAMFile) {
+        return hasCRAMFileContents(putativeCRAMFile.toPath());
+    }
+
     public static boolean isNonPrimary(GATKRead read) {
         return read.isSecondaryAlignment() || read.isSupplementaryAlignment() || read.isUnmapped();
     }

src/main/java/org/broadinstitute/hellbender/utils/test/SamAssertionUtils.java

@@ -14,6 +14,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.LinkedHashMap;
@@ -36,7 +37,9 @@ public final class SamAssertionUtils {
     private static SamReader getReader(final File sam, final ValidationStringency validationStringency, final File reference) {
         return SamReaderFactory.makeDefault().validationStringency(validationStringency).referenceSequence(reference).open(sam);
     }
-
+    private static SamReader getReader(final Path sam, final ValidationStringency validationStringency, final Path reference) {
+        return SamReaderFactory.makeDefault().validationStringency(validationStringency).referenceSequence(reference).open(sam);
+    }
     /**
      *  causes an exception if the given sam files aren't equal
      *  @param actualSam the actual file
@@ -45,8 +48,12 @@ private static SamReader getReader(final File sam, final ValidationStringency va
      *  @param reference is allowed to be null
      */
     public static void assertSamsEqual(final File actualSam, final File expectedSam, final ValidationStringency validationStringency, final File reference) throws IOException {
+        assertSamsEqual(actualSam.toPath(), expectedSam.toPath(), validationStringency,
+                (null==reference?null:reference.toPath()));
+    }
+    public static void assertSamsEqual(final Path actualSam, final Path expectedSam, final ValidationStringency validationStringency, final Path reference) throws IOException {
         final String equalStringent = samsEqualStringent(actualSam, expectedSam, validationStringency, reference);
-        Assert.assertNull(equalStringent, "SAM file " + actualSam.getPath() + " differs from expected output:" + expectedSam.getPath() + " " + equalStringent);
+        Assert.assertNull(equalStringent, "SAM file " + actualSam.toUri().toString() + " differs from expected output:" + expectedSam.toUri().toString() + " " + equalStringent);
     }
 
     /**
@@ -68,6 +75,9 @@ public static void assertSamsEqual(final File actualSam, final File expectedSam,
     public static void assertSamsEqual(final File actualSam, final File expectedSam, final File reference) throws IOException {
         assertSamsEqual(actualSam, expectedSam, ValidationStringency.DEFAULT_STRINGENCY, reference);
     }
+    public static void assertSamsEqual(final Path actualSam, final Path expectedSam, final Path reference) throws IOException {
+        assertSamsEqual(actualSam, expectedSam, ValidationStringency.DEFAULT_STRINGENCY, reference);
+    }
 
     /**
      * causes an exception if the given sam files aren't equal
@@ -145,6 +155,19 @@ public static String samsEqualLenient(final File actualSam, final File expectedS
      * @return null if equal or message string if not equal.
      */
     public static String samsEqualStringent(final File actualSam, final File expectedSam, final ValidationStringency validation, final File reference) throws IOException {
+        return samsEqualStringent(actualSam.toPath(), expectedSam.toPath(), validation, (null==reference?null:reference.toPath()));
+    }
+
+    /**
+     * Compares SAM/BAM files in a stringent way but not by byte identity (allow reorder of attributes)
+     * Comparing by MD5s is too strict and comparing by SamComparison is too lenient. So we need this method.
+     *
+     * This differs from a byte-to-byte comparison:
+     * - @PG and @CO lines in headers are ignored in the comparison.
+     * - each read in the actual file are allowed to have a superset of the attributes of the corresponding read in the expected set
+     * @return null if equal or message string if not equal.
+     */
+    public static String samsEqualStringent(final Path actualSam, final Path expectedSam, final ValidationStringency validation, final Path reference) throws IOException {
         if (sameMD5s(actualSam, expectedSam)) {
             return null;
         }
@@ -168,7 +191,22 @@ private static boolean sameMD5s(final File actualSam, final File expectedSam) th
         return fileMD5_1.equals(fileMD5_2);
     }
 
+
+    private static boolean sameMD5s(final Path actualSam, final Path expectedSam) throws IOException {
+        final String fileMD5_1 = Utils.calculatePathMD5(actualSam);
+        final String fileMD5_2 = Utils.calculatePathMD5(expectedSam);
+        return fileMD5_1.equals(fileMD5_2);
+    }
+
     private static String compareReads(final File actualSam, final File expectedSam, final ValidationStringency validation, final File reference) throws IOException {
+        return compareReads(
+                actualSam.toPath(),
+                expectedSam.toPath(),
+                validation,
+                (null==reference?null:reference.toPath()));
+    }
+
+    private static String compareReads(final Path actualSam, final Path expectedSam, final ValidationStringency validation, final Path reference) throws IOException {
         try(final SamReader reader1 = getReader(actualSam, validation, reference);
             final SamReader reader2 = getReader(expectedSam, validation, reference)) {
             final SAMRecordIterator it1 = reader1.iterator();
@@ -189,9 +227,9 @@ private static String compareReads(final File actualSam, final File expectedSam,
         }
     }
 
-    private static String equalHeadersIgnoreCOandPG(final File actualSam, final File expectedSam, final ValidationStringency validation, final File reference) throws IOException {
+    private static String equalHeadersIgnoreCOandPG(final Path actualSam, final Path expectedSam, final ValidationStringency validation, final Path reference) throws IOException {
         try(final SamReader reader1 = getReader(actualSam, validation, reference);
-            final SamReader reader2 = getReader(expectedSam, validation, reference)){
+                final SamReader reader2 = getReader(expectedSam, validation, reference)){
 
             final SAMFileHeader h1 = reader1.getFileHeader();
             final SAMFileHeader h2 = reader2.getFileHeader();
@@ -376,16 +414,24 @@ public static void assertEqualBamFiles(
      * Validate/assert that the contents are CRAM if the extension is .cram
      */
     public static void assertCRAMContentsIfCRAM(final File putativeCRAMFile) {
-        if (IOUtils.isCramFile(putativeCRAMFile)) {
-            assertCRAMContents(putativeCRAMFile);
+        Path path = (null==putativeCRAMFile?null:putativeCRAMFile.toPath());
+        assertCRAMContentsIfCRAM(path);
+    }
+
+    /**
+     * Validate/assert that the contents are CRAM if the extension is .cram
+     */
+    public static void assertCRAMContentsIfCRAM(final Path putativeCRAMPath) {
+        if (IOUtils.isCramFile(putativeCRAMPath)) {
+            assertCRAMContents(putativeCRAMPath);
         }
     }
 
     /**
      * Unconditionally validate/assert that the contents are CRAM
      */
-    public static void assertCRAMContents(final File putativeCRAMFile) {
-        Assert.assertTrue(ReadUtils.hasCRAMFileContents(putativeCRAMFile), "should have had CRAM contents: " + putativeCRAMFile.getName());
+    public static void assertCRAMContents(final Path putativeCRAMPath) {
+        Assert.assertTrue(ReadUtils.hasCRAMFileContents(putativeCRAMPath), "should have had CRAM contents: " + putativeCRAMPath.toUri().toString());
     }
 
     private static void sortSam(final File input, final File output, final File reference, final ValidationStringency stringency) {

src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/ApplyBQSRIntegrationTest.java

@@ -1,12 +1,18 @@
 package org.broadinstitute.hellbender.tools.walkers.bqsr;
 
+import com.google.common.jimfs.Configuration;
+import com.google.common.jimfs.Jimfs;
 import htsjdk.samtools.SamReaderFactory;
+import java.nio.file.FileSystem;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import org.apache.commons.lang.StringUtils;
 import org.broadinstitute.barclay.argparser.CommandLineException;
 import org.broadinstitute.hellbender.CommandLineProgramTest;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.GATKBaseTest;
+import org.broadinstitute.hellbender.utils.gcs.BucketUtils;
 import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec;
 import org.broadinstitute.hellbender.utils.test.SamAssertionUtils;
 import org.testng.Assert;
@@ -80,8 +86,18 @@ public Object[][] createABQSRTestData() {
         return tests.toArray(new Object[][]{});
     }
 
+    @DataProvider(name = "MiniApplyBQSRTest")
+    public Object[][] createMiniABQSRTestData() {
+        List<Object[]> tests = new ArrayList<>();
+
+        //Note: these outputs were created using GATK3
+        tests.add(new Object[]{new ABQSRTest(hiSeqBam, null, ".bam", null, resourceDir + "expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam")});
+
+        return tests.toArray(new Object[][]{});
+    }
+
     @Test(dataProvider = "ApplyBQSRTest")
-    public void testApplyBQSR(ABQSRTest params) throws IOException {
+    public void testApplyBQSRFile(ABQSRTest params) throws IOException {
         File outFile = GATKBaseTest.createTempFile("applyBQSRTest", params.outputExtension);
         final ArrayList<String> args = new ArrayList<>();
         File refFile = null;
@@ -90,18 +106,77 @@ public void testApplyBQSR(ABQSRTest params) throws IOException {
         args.add(new File(params.bam).getAbsolutePath());
         args.add("--" + StandardArgumentDefinitions.BQSR_TABLE_LONG_NAME);
         args.add(new File(resourceDir + "HiSeq.20mb.1RG.table.gz").getAbsolutePath());
-        args.add("-O"); args.add(outFile.getAbsolutePath());
+        args.add("-O");
+        args.add(outFile.getAbsolutePath());
         if (params.reference != null) {
             refFile = new File(params.reference);
-            args.add("-R"); args.add(refFile.getAbsolutePath());
+            args.add("-R");
+            args.add(refFile.getAbsolutePath());
+            if (params.args != null) {
+                Stream.of(params.args).forEach(arg -> args.add(arg));
+            }
+
+            runCommandLine(args);
+
+            SamAssertionUtils.assertSamsEqual(outFile, new File(params.expectedFile), refFile);
+        }
+    }
+
+    @Test(dataProvider = "MiniApplyBQSRTest")
+    public void testApplyBQSRPath(ABQSRTest params) throws IOException {
+        try (FileSystem jimfs = Jimfs.newFileSystem(Configuration.unix())) {
+            final Path outPath = jimfs.getPath("applyBQSRTest"+params.outputExtension);
+
+            final ArrayList<String> args = new ArrayList<>();
+            Path refPath = null;
+
+            args.add("-I");
+            args.add(new File(params.bam).getAbsolutePath());
+            args.add("--" + StandardArgumentDefinitions.BQSR_TABLE_LONG_NAME);
+            args.add(new File(resourceDir + "HiSeq.20mb.1RG.table.gz").getAbsolutePath());
+            args.add("-O"); args.add(outPath.toUri().toString());
+            if (params.reference != null) {
+                File refFile = new File(params.reference);
+                args.add("-R"); args.add(refFile.getAbsolutePath());
+                refPath = refFile.toPath();
+            }
+            if (params.args != null) {
+                Stream.of(params.args).forEach(arg -> args.add(arg));
+            }
+
+            runCommandLine(args);
+
+            SamAssertionUtils.assertSamsEqual(outPath, new File(params.expectedFile).toPath(), refPath);
+        }
+    }
+
+    @Test(dataProvider = "ApplyBQSRTest", groups={"bucket"})
+    public void testApplyBQSRCloud(ABQSRTest params) throws IOException {
+        // getTempFilePath also deletes the file on exit.
+        final String outString = BucketUtils.getTempFilePath(getGCPTestStaging() + "tmp/testApplyBQSRCloud",  params.outputExtension);
+        final Path outPath = BucketUtils.getPathOnGcs(outString);
+        final ArrayList<String> args = new ArrayList<>();
+        Path refPath = null;
+
+        args.add("-I");
+        args.add(new File(params.bam).getAbsolutePath());
+        args.add("--" + StandardArgumentDefinitions.BQSR_TABLE_LONG_NAME);
+        args.add(new File(resourceDir + "HiSeq.20mb.1RG.table.gz").getAbsolutePath());
+        args.add("-O");
+        args.add(outString);
+        if (params.reference != null) {
+            File refFile = new File(params.reference);
+            args.add("-R");
+            args.add(refFile.getAbsolutePath());
+            refPath = refFile.toPath();
         }
         if (params.args != null) {
             Stream.of(params.args).forEach(arg -> args.add(arg));
         }
 
         runCommandLine(args);
 
-        SamAssertionUtils.assertSamsEqual(outFile, new File(params.expectedFile), refFile);
+        SamAssertionUtils.assertSamsEqual(outPath, new File(params.expectedFile).toPath(), refPath);
     }
 
     @Test

src/test/java/org/broadinstitute/hellbender/utils/test/SamAssertionUtilsUnitTest.java

@@ -61,12 +61,12 @@ public Object[][] testCRAMContentsFailData() {
 
     @Test(dataProvider = "testCRAMContentsSucceed")
     public void testAssertCRAMContentsSucceed(File putativeCRAMFile) {
-        SamAssertionUtils.assertCRAMContents(putativeCRAMFile);
+        SamAssertionUtils.assertCRAMContents(putativeCRAMFile.toPath());
     }
 
     @Test(dataProvider = "testCRAMContentsFail", expectedExceptions=AssertionError.class)
     public void testAssertCRAMContentsFail(File putativeCRAMFile) {
-        SamAssertionUtils.assertCRAMContents(putativeCRAMFile);
+        SamAssertionUtils.assertCRAMContents(putativeCRAMFile.toPath());
     }
 
     @DataProvider(name="testCRAMContentsIfCRAMSucceed")