Java IOUtil.createTempDir方法代码示例

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
/**
 * Divide the part files into the batches to download and pre-sort at the same time.
 *
 * @param partFiles all part files to download.
 *
 * @return a map of path to download the parts and the parts that should be used (as reads
 * source).
 *
 * @see #downloadBatchesAndPreSort(List)
 */
private Map<Path, ReadsDataSource> divideIntoBatches(final List<Path> partFiles) {
    // partition the files into batches
    final List<List<Path>> batches = Lists.partition(partFiles, numberOfParts);
    final Map<Path, ReadsDataSource> toReturn = new LinkedHashMap<>(batches.size());

    // creates a temp file for each in a common temp folder
    final File tempDir = IOUtil.createTempDir(this.toString(), ".batches");
    int i = 0;
    for (final List<Path> parts : batches) {
        // create a temp file and store it in the temp parts
        final Path tempFile =
                IOUtils.getPath(new File(tempDir, "batch-" + i++ + ".bam").getAbsolutePath());
        logger.debug("Batch file {} will contain {} parts: {}",
                () -> tempFile.toUri().toString(),
                () -> parts.size(),
                () -> parts.stream().map(p -> p.toUri().toString())
                        .collect(Collectors.toList()));
        toReturn.put(tempFile, new ReadsDataSource(parts, getSamReaderFactory()));
    }

    return toReturn;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test(dataProvider = "inputs")
public void testBamToBfq(final File input, final boolean isPairedRun,
                 final String outputFilePrefix) throws IOException {
    final File analysisDir = IOUtil.createTempDir("BamToBfqTest", ".dir");
    try {
        final String[] args = new String[] {
                "INPUT=" + input.getAbsolutePath(),
                "ANALYSIS_DIR=" + analysisDir.getAbsolutePath(),
                "OUTPUT_FILE_PREFIX=" + outputFilePrefix,
                "PAIRED_RUN=" + isPairedRun,
                "READS_TO_ALIGN=8"
        };
        BamToBfq bamToBfq = new BamToBfq();
        Assert.assertEquals(bamToBfq.instanceMain(args), 0, "Can't process " + input.getAbsolutePath() + " correctly");

        final File output = new File(analysisDir, outputFilePrefix + ".0.1.bfq");
        final File expectedBFQ = new File(TEST_DATA_DIR, outputFilePrefix + ".0.1.bfq");

        Assert.assertEquals(Files.readAllBytes(output.toPath()), Files.readAllBytes(expectedBFQ.toPath()));
    } finally {
        TestUtil.recursiveDelete(analysisDir);
    }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void fullBclParserTestWDeletedSkipsImpl(final int[] tiles, final int size, final int seekAfter, final int newTileIndex, final int orderedTileIndex, final String readStructure) {
    final File basecallDir = IOUtil.createTempDir("bclParserTest", "BaseCalls");

    Exception exc = null;
    try {
        final File l001 = new File(basecallDir, "L001");
        if (!l001.mkdir()) {
            throw new RuntimeException("Couldn't make lane dir " + l001.getAbsolutePath());
        }

        copyBcls(TEST_DATA_DIR, l001);
        deleteBclFiles(l001, readStructure);
        fullBclParserTestImpl(l001, READ_STRUCTURE_WSKIPS, tiles, size, seekAfter, newTileIndex, orderedTileIndex, false);
    } catch (final Exception thrExc) {
        exc = thrExc;
    } finally {
        IOUtil.deleteDirectoryTree(basecallDir);
    }
    if (exc != null) {
        if (exc.getClass() == PicardException.class) {
            throw new PicardException(exc.getMessage());
        }
        throw new RuntimeException(exc);
    }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@BeforeMethod
private void setUp() throws Exception {
    illuminaDir = IOUtil.createTempDir("ift_test", "IlluminaDir");

    interopDir = new File(illuminaDir, "InterOp");
    if (!interopDir.exists() && !interopDir.mkdir()) {
        throw new RuntimeException("Couldn't make interop dir " + interopDir.getAbsolutePath());
    }

    dataDir = new File(illuminaDir, "Data");
    if (!dataDir.exists() && !dataDir.mkdir()) {
        throw new RuntimeException("Couldn't make data dir " + dataDir.getAbsolutePath());
    }

    intensityDir = new File(dataDir, "Intensities");
    if (!intensityDir.exists() && !intensityDir.mkdir()) {
        throw new RuntimeException("Couldn't make intensity dir " + intensityDir.getAbsolutePath());
    }

    basecallDir = new File(intensityDir, "BaseCalls");
    if (!basecallDir.exists() && !basecallDir.mkdir()) {
        throw new RuntimeException("Couldn't make basecalls dir " + basecallDir.getAbsolutePath());
    }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test(dataProvider = "testLaneMetrics")
public void testWriteLaneMetrics(final String testRun) throws Exception {
    for (final boolean useReadStructure : Arrays.asList(true, false)) {
        final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
        clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
        clp.RUN_DIRECTORY = new File(TEST_DIRECTORY, testRun);
        clp.OUTPUT_PREFIX = "test";
        if (useReadStructure) clp.READ_STRUCTURE = new ReadStructure("101T8B101T");
        clp.doWork();

        final File laneMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaLaneMetrics.getExtension());
        final File canonicalOutputFile = buildOutputFile(TEST_DIRECTORY, testRun, IlluminaLaneMetrics.getExtension());

        IOUtil.assertFilesEqual(canonicalOutputFile, laneMetricsFile);

        IOUtil.deleteDirectoryTree(clp.OUTPUT_DIRECTORY);
    }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test(dataProvider = "testCollectIlluminaLaneMetrics")
public void testCollectIlluminaLaneMetrics(final String testRun, final ReadStructure readStructure, final boolean isNovaSeq) throws Exception {
    for (final boolean useReadStructure : Arrays.asList(true, false)) {
        final File runDirectory = new File(TILE_RUN_DIRECTORY, testRun);
        final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
        clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
        clp.RUN_DIRECTORY = runDirectory;
        clp.OUTPUT_PREFIX = "test";
        clp.IS_NOVASEQ = isNovaSeq;
        if (useReadStructure) clp.READ_STRUCTURE = readStructure;
        clp.doWork();

        final File phasingMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaPhasingMetrics.getExtension());
        final File canonicalPhasingFile = buildOutputFile(runDirectory, testRun, IlluminaPhasingMetrics.getExtension());
        IOUtil.assertFilesEqual(canonicalPhasingFile, phasingMetricsFile);

        final File laneMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaLaneMetrics.getExtension());
        final File canonicalLaneFile = buildOutputFile(runDirectory, testRun, IlluminaLaneMetrics.getExtension());
        IOUtil.assertFilesEqual(canonicalLaneFile, laneMetricsFile);
        IOUtil.deleteDirectoryTree(clp.OUTPUT_DIRECTORY);
    }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
/** Ensures that an exception is thrown when we encounter a tile without phasing/pre-phasing metrics. */
@Test(expectedExceptions = PicardException.class)
public void testMissingPhasingValuesStrict() {
    final ReadStructure readStructure = new ReadStructure("151T8B8B151T");
    for (final boolean useReadStructure : Arrays.asList(true, false)) {
        final File runDirectory = TEST_MISSING_PHASING_DIRECTORY;
        final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
        clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
        clp.RUN_DIRECTORY = runDirectory;
        clp.OUTPUT_PREFIX = "test";
        clp.VALIDATION_STRINGENCY = ValidationStringency.STRICT;
        if (useReadStructure) clp.READ_STRUCTURE = readStructure;
        clp.doWork();

        final File phasingMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaPhasingMetrics.getExtension());
        final File canonicalPhasingFile = buildOutputFile(runDirectory, runDirectory.getName(), IlluminaPhasingMetrics.getExtension());
        IOUtil.assertFilesEqual(canonicalPhasingFile, phasingMetricsFile);

        final File laneMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaLaneMetrics.getExtension());
        final File canonicalLaneFile = buildOutputFile(runDirectory, runDirectory.getName(), IlluminaLaneMetrics.getExtension());
        IOUtil.assertFilesEqual(canonicalLaneFile, laneMetricsFile);
        IOUtil.deleteDirectoryTree(clp.OUTPUT_DIRECTORY);
    }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
/** Silently continue if we encounter a tile without phasing/pre-phasing metrics. */
@Test
public void testMissingPhasingValuesSilent() throws IOException {
    final ReadStructure readStructure = new ReadStructure("151T8B8B151T");
    for (final boolean useReadStructure : Arrays.asList(true, false)) {
        final File runDirectory = TEST_MISSING_PHASING_DIRECTORY;
        final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
        clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
        clp.RUN_DIRECTORY = runDirectory;
        clp.OUTPUT_PREFIX = "test";
        clp.VALIDATION_STRINGENCY = ValidationStringency.SILENT;
        if (useReadStructure) clp.READ_STRUCTURE = readStructure;
        clp.doWork();

        final File phasingMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaPhasingMetrics.getExtension());
        final File canonicalPhasingFile = buildOutputFile(runDirectory, runDirectory.getName(), IlluminaPhasingMetrics.getExtension());
        IOUtil.assertFilesEqual(canonicalPhasingFile, phasingMetricsFile);

        final File laneMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaLaneMetrics.getExtension());
        final File canonicalLaneFile = buildOutputFile(runDirectory, runDirectory.getName(), IlluminaLaneMetrics.getExtension());
        IOUtil.assertFilesEqual(canonicalLaneFile, laneMetricsFile);
        IOUtil.deleteDirectoryTree(clp.OUTPUT_DIRECTORY);
    }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test(dataProvider = "testOpticalDuplicateDetectionDataProvider")
public void testOpticalDuplicateDetection(final File sam, final long expectedNumOpticalDuplicates) {
    final File outputDir = IOUtil.createTempDir(TEST_BASE_NAME + ".", ".tmp");
    outputDir.deleteOnExit();
    final File outputSam = new File(outputDir, TEST_BASE_NAME + ".sam");
    outputSam.deleteOnExit();
    final File metricsFile = new File(outputDir, TEST_BASE_NAME + ".duplicate_metrics");
    metricsFile.deleteOnExit();
    // Run MarkDuplicates, merging the 3 input files, and either enabling or suppressing PG header
    // record creation according to suppressPg.
    final MarkDuplicates markDuplicates = new MarkDuplicates();
    markDuplicates.setupOpticalDuplicateFinder();
    markDuplicates.INPUT = CollectionUtil.makeList(sam.getAbsolutePath());
    markDuplicates.OUTPUT = outputSam;
    markDuplicates.METRICS_FILE = metricsFile;
    markDuplicates.TMP_DIR = CollectionUtil.makeList(outputDir);
    // Needed to suppress calling CommandLineProgram.getVersion(), which doesn't work for code not in a jar
    markDuplicates.PROGRAM_RECORD_ID = null;
    Assert.assertEquals(markDuplicates.doWork(), 0);
    Assert.assertEquals(markDuplicates.numOpticalDuplicates(), expectedNumOpticalDuplicates);
    TestUtil.recursiveDelete(outputDir);

}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test(dataProvider = "testOpticalDuplicateDetectionDataProvider")
public void testOpticalDuplicateDetection(final File sam, final File reference, final String outputExtension, final long expectedNumOpticalDuplicates) {
    final File outputDir = IOUtil.createTempDir(TEST_BASE_NAME + ".", ".tmp");
    outputDir.deleteOnExit();
    final File outputSam = new File(outputDir, TEST_BASE_NAME + outputExtension);
    outputSam.deleteOnExit();
    final File metricsFile = new File(outputDir, TEST_BASE_NAME + ".duplicate_metrics");
    metricsFile.deleteOnExit();
    // Run MarkDuplicatesGATK, merging the 3 input files, and either enabling or suppressing PG header
    // record creation according to suppressPg.
    final MarkDuplicatesGATK markDuplicatesGATK = new MarkDuplicatesGATK();
    markDuplicatesGATK.setupOpticalDuplicateFinder();
    markDuplicatesGATK.INPUT = CollectionUtil.makeList(sam);
    if (null != reference) {
        markDuplicatesGATK.REFERENCE_SEQUENCE = reference;
    }
    markDuplicatesGATK.OUTPUT = outputSam;
    markDuplicatesGATK.METRICS_FILE = metricsFile;
    markDuplicatesGATK.TMP_DIR = CollectionUtil.makeList(outputDir);
    // Needed to suppress calling CommandLineProgram.getVersion(), which doesn't work for code not in a jar
    markDuplicatesGATK.PROGRAM_RECORD_ID = null;
    Assert.assertEquals(markDuplicatesGATK.doWork(), null);
    Assert.assertEquals(markDuplicatesGATK.numOpticalDuplicates(), expectedNumOpticalDuplicates);
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test(dataProvider = "testDuplicateDetectionDataProvider")
public void testDuplicateDetection(final File sam, final long expectedNumOpticalDuplicates) {
    final File outputDir = IOUtil.createTempDir(TEST_BASE_NAME + ".", ".tmp");
    outputDir.deleteOnExit();
    final File outputSam = new File(outputDir, TEST_BASE_NAME + ".sam");
    outputSam.deleteOnExit();
    final File metricsFile = new File(outputDir, TEST_BASE_NAME + ".duplicate_metrics");
    metricsFile.deleteOnExit();
    // Run MarkDuplicatesGATK, merging the 3 input files, and either enabling or suppressing PG header
    // record creation according to suppressPg.
    final MarkDuplicatesGATK markDuplicatesGATK = new MarkDuplicatesGATK();
    markDuplicatesGATK.setupOpticalDuplicateFinder();
    markDuplicatesGATK.INPUT = CollectionUtil.makeList(sam);
    markDuplicatesGATK.OUTPUT = outputSam;
    markDuplicatesGATK.METRICS_FILE = metricsFile;
    markDuplicatesGATK.TMP_DIR = CollectionUtil.makeList(outputDir);
    // Needed to suppress calling CommandLineProgram.getVersion(), which doesn't work for code not in a jar
    markDuplicatesGATK.PROGRAM_RECORD_ID = null;
    Assert.assertEquals(markDuplicatesGATK.doWork(), null);
    Assert.assertEquals(markDuplicatesGATK.numOpticalDuplicates(), expectedNumOpticalDuplicates);
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
private SortingCollection<String> makeSortingCollection() {
    final String name = getClass().getSimpleName();
    final File tmpDir = IOUtil.createTempDir(name, null);
    tmpDir.deleteOnExit();
    // 256 byte for one name, and 1/10 part of all memory for this, rough estimate
    long maxNamesInRam = Runtime.getRuntime().maxMemory() / 256 / 10;
    return SortingCollection.newInstance(
            String.class,
            new StringCodec(),
            String::compareTo,
            (int) Math.min(maxNamesInRam, Integer.MAX_VALUE),
            tmpDir
    );
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@BeforeMethod
private void setUp() throws Exception {
    intensityDir = IOUtil.createTempDir("ift_test", "Intensities");
    basecallDir = new File(intensityDir, "BaseCalls");
    if (!basecallDir.mkdir()) {
        throw new RuntimeException("Couldn't make basecalls dir " + basecallDir.getAbsolutePath());
    }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test(dataProvider = "testHasCbclsDataProvider")
public void testHasCbcls(final int lane,
                         final boolean createCbclDir,
                         final boolean createCbcl,
                         final boolean expectedResult) throws IOException {

    final File basecallsDir = IOUtil.createTempDir("basecalls", "");
    basecallsDir.deleteOnExit();

    if (0 < lane) {
        final File laneDir = new File(basecallsDir, IlluminaFileUtil.longLaneStr(lane));
        Assert.assertTrue(laneDir.mkdir());

        if (createCbclDir) {
            final File cbclDir = new File(laneDir, "C1.1");
            cbclDir.mkdirs();
            cbclDir.deleteOnExit();

            if (createCbcl) {
                final File cbcl = new File(cbclDir, IlluminaFileUtil.longLaneStr(lane) + "_42.cbcl");
                new FileOutputStream(cbcl).close();
                cbcl.deleteOnExit();
            }
        }
    }

    Assert.assertEquals(IlluminaFileUtil.hasCbcls(basecallsDir, lane), expectedResult);
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@BeforeTest
void setup() throws IOException {
    File OUTPUT_DATA_PATH = IOUtil.createTempDir("FixVcfHeaderTest", null);
    OUTPUT_DATA_PATH.deleteOnExit();
    final File testDataPath      = new File("testdata/picard/vcf/FixVcfHeaderTest/");
    INPUT_VCF                    = new File(testDataPath, "input.vcf");
    OUTPUT_VCF                   = new File(testDataPath, "output.vcf");
    HEADER_VCF                   = new File(testDataPath, "header.vcf");
    HEADER_VCF_WITH_EXTRA_SAMPLE = new File(testDataPath, "header_with_extra_sample.vcf");
}