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);
}
}
}
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);
}
}
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);
}
}
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);
}
}
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);
}
}
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);
}
}
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);
}
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);
}
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);
}
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);
}
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);
}
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);
}
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);
}
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);
}
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);
}