本文整理汇总了Java中htsjdk.samtools.util.IOUtil.createTempDir方法的典型用法代码示例。如果您正苦于以下问题:Java IOUtil.createTempDir方法的具体用法?Java IOUtil.createTempDir怎么用?Java IOUtil.createTempDir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.createTempDir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: divideIntoBatches
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;
}
示例2: testBamToBfq
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);
}
}
示例3: 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4: setUp
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());
}
}
示例5: 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6: 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7: 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8: 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9: testOpticalDuplicateDetection
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);
}
示例10: testOpticalDuplicateDetection
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);
}
示例11: testDuplicateDetection
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);
}
示例12: makeSortingCollection
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
);
}
示例13: setUp
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());
}
}
示例14: testHasCbcls
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);
}
示例15: setup
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");
}