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Java IOUtil.deleteDirectoryTree方法代码示例

本文整理汇总了Java中htsjdk.samtools.util.IOUtil.deleteDirectoryTree方法的典型用法代码示例。如果您正苦于以下问题：Java IOUtil.deleteDirectoryTree方法的具体用法？Java IOUtil.deleteDirectoryTree怎么用？Java IOUtil.deleteDirectoryTree使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类htsjdk.samtools.util.IOUtil的用法示例。


在下文中一共展示了IOUtil.deleteDirectoryTree方法的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。

示例1: deleteRelativeFiles

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public static void deleteRelativeFiles(final File baseFile, final List<String> relativeFilesToDelete) {
    for (final String relativeFile : relativeFilesToDelete) {
        final File actualFile = new File(baseFile, relativeFile);


        if (!actualFile.exists()) {
            throw new RuntimeException("Trying to delete a non-existent file" + actualFile.getAbsolutePath());
        }

        if (actualFile.isDirectory()) {
            IOUtil.deleteDirectoryTree(actualFile);
        } else {
            IOUtil.deleteFiles(actualFile);
        }
        if (actualFile.exists()) {
            throw new RuntimeException("File still exists after calling delete: " + actualFile);
        }
    }
}
开发者ID:broadinstitute，项目名称:picard，代码行数:20，代码来源:IlluminaFileUtilTest.java

示例2: fullBclParserTestWDeletedSkipsImpl

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);
    }
}
开发者ID:broadinstitute，项目名称:picard，代码行数:26，代码来源:BclParserTest.java

示例3: testWriteLaneMetrics

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);
    }
}
开发者ID:broadinstitute，项目名称:picard，代码行数:19，代码来源:IlluminaLaneMetricsCollectorTest.java

示例4: testCollectIlluminaLaneMetrics

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);
    }
}
开发者ID:broadinstitute，项目名称:picard，代码行数:23，代码来源:IlluminaLaneMetricsCollectorTest.java

示例5: testMissingPhasingValuesStrict

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);
    }
}
开发者ID:broadinstitute，项目名称:picard，代码行数:25，代码来源:IlluminaLaneMetricsCollectorTest.java

示例6: testMissingPhasingValuesSilent

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);
    }
}
开发者ID:broadinstitute，项目名称:picard，代码行数:25，代码来源:IlluminaLaneMetricsCollectorTest.java

示例7: tearDown

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@AfterTest
private void tearDown() {
    IOUtil.deleteDirectoryTree(basecallsDir);
    IOUtil.deleteDirectoryTree(dual);
    IOUtil.deleteDirectoryTree(qual);
    IOUtil.deleteDirectoryTree(noSymlink);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:8，代码来源:ExtractIlluminaBarcodesTest.java

示例8: tearDown

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@AfterMethod
private void tearDown() {
    IOUtil.deleteDirectoryTree(dataDir);
    IOUtil.deleteDirectoryTree(basecallDir);
    IOUtil.deleteDirectoryTree(intensityDir);
    IOUtil.deleteDirectoryTree(illuminaDir);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:8，代码来源:CheckIlluminaDirectoryTest.java

示例9: tearDown

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@AfterMethod
private void tearDown() {
    IOUtil.deleteDirectoryTree(intensityDir);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:5，代码来源:IlluminaFileUtilTest.java

示例10: tearDown

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@AfterTest
private void tearDown() {
    IOUtil.deleteDirectoryTree(rootTestDir);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:5，代码来源:CollectIlluminaBasecallingMetricsTest.java

示例11: tearDown

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@AfterTest
private void tearDown() {
    IOUtil.deleteDirectoryTree(tempDir);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:5，代码来源:DownsampleSamTest.java

示例12: teardown

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@AfterClass
public void teardown() {
	IOUtil.deleteDirectoryTree(OUTPUT_DATA_PATH);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:5，代码来源:SplitVcfsTest.java

示例13: teardown

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@AfterClass
public void teardown() {
    IOUtil.deleteDirectoryTree(OUTPUT_DATA_PATH);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:5，代码来源:UpdateVcfSequenceDictionaryTest.java

示例14: tearDown

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@AfterClass
public void tearDown() {
    IOUtil.deleteDirectoryTree(OUTPUT_DATA_PATH);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:5，代码来源:GenotypeConcordanceTest.java

示例15: rmTemp

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@AfterClass
private void rmTemp() {
    IOUtil.deleteDirectoryTree(tempFolder);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:5，代码来源:CheckFingerprintTest.java


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