本文整理汇总了Java中htsjdk.samtools.util.IOUtil类的典型用法代码示例。如果您正苦于以下问题:Java IOUtil类的具体用法?Java IOUtil怎么用?Java IOUtil使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
IOUtil类属于htsjdk.samtools.util包,在下文中一共展示了IOUtil类的20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,您的评价将有助于我们的系统推荐出更棒的Java代码示例。
示例1: unrollFileCollection
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
/** return 'inputs' as set, if a filename ends with '*.list'
* is is considered as a file:one file per line
* @param inputs files
* @return set of files
*/
public static LinkedHashSet<File> unrollFileCollection(java.util.Collection<File> inputs)
{
LinkedHashSet<File> vcfFiles= new LinkedHashSet<>(inputs.size()+1);
for(File file : inputs)
{
if(file.getName().endsWith(".list"))
{
IOUtil.assertFileIsReadable(file);
for (final String s : IOUtil.readLines(file))
{
if (s.endsWith("#")) continue;
if (s.trim().isEmpty()) continue;
vcfFiles.add(new File(s));
}
}
else
{
vcfFiles.add(file);
}
}
return vcfFiles;
}
开发者ID:dariober,项目名称:ASCIIGenome,代码行数:29,代码来源:IOUtils.java
示例2: getMaybeBufferedOutputStream
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
/**
* Creates a maybe buffered output stream from a Path.
*
* In addition, if the Path is from the Hadoop Filesystem, it sets other characteristics for
* the output stream:
*
* - HDFS Block-size: {@link #hdfsBlockSize}.
* - Buffer-size: {@link #bufferSize}, instead of wrapping in a buffered stream.
*/
private OutputStream getMaybeBufferedOutputStream(final Path path) throws IOException {
// iif there is a block-size to change and the path is from Hadoop
if (hdfsBlockSize != null && path instanceof HadoopPath) {
final HadoopPath hadoopPath = (HadoopPath) path;
// gets the HDFS to create the output stream with custom block-size
final FileSystem hdfs = hadoopPath.getFileSystem().getHDFS();
// gets the the path (extracted here to get the default replication)
final org.apache.hadoop.fs.Path hdfsPath = hadoopPath.getRawResolvedPath();
// construct the output stream already buffered here
return hdfs.create(hdfsPath, forceOverwrite,
// buffer size
bufferSize,
// replication is using the default
hdfs.getDefaultReplication(hdfsPath),
// block-size is the one set here
hdfsBlockSize);
}
logger.debug("Block-size is ignored: {}", () -> hdfsBlockSize);
return IOUtil.maybeBufferOutputStream(Files.newOutputStream(path), bufferSize);
}
开发者ID:magicDGS,项目名称:ReadTools,代码行数:31,代码来源:ReadWriterFactory.java
示例3: divideIntoBatches
import htsjdk.samtools.util.IOUtil; //导入依赖的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;
}
开发者ID:magicDGS,项目名称:ReadTools,代码行数:33,代码来源:DistmapPartDownloader.java
示例4: BamToBfqWriter
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
/**
* Constructor
*
* @param bamFile the BAM file to read from
* @param outputPrefix the directory and file prefix for the binary fastq files
* @param total the total number of records that should be written, drawn evenly
* from throughout the file (null for all).
* @param chunk the maximum number of records that should be written to any one file
* @param pairedReads whether these reads are from a paired-end run
* @param namePrefix The string to be stripped off the read name
* before writing to the bfq file. May be null, in which case
* the name will not be trimmed.
* @param includeNonPfReads whether to include non pf-reads
* @param clipAdapters whether to replace adapters as marked with XT:i clipping position attribute
*/
public BamToBfqWriter(final File bamFile, final String outputPrefix, final Integer total,
final Integer chunk, final boolean pairedReads, String namePrefix,
boolean includeNonPfReads, boolean clipAdapters, Integer basesToWrite) {
IOUtil.assertFileIsReadable(bamFile);
this.bamFile = bamFile;
this.outputPrefix = outputPrefix;
this.pairedReads = pairedReads;
if (total != null) {
final double writeable = (double)countWritableRecords();
this.increment = (int)Math.floor(writeable/total.doubleValue());
if (this.increment == 0) {
this.increment = 1;
}
}
if (chunk != null) {
this.chunk = chunk;
}
this.namePrefix = namePrefix;
this.nameTrim = namePrefix != null ? namePrefix.length() : 0;
this.includeNonPfReads = includeNonPfReads;
this.clipAdapters = clipAdapters;
this.basesToWrite = basesToWrite;
}
开发者ID:broadinstitute,项目名称:picard,代码行数:40,代码来源:BamToBfqWriter.java
示例5: customCommandLineValidation
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
@Override
protected String[] customCommandLineValidation() {
IOUtil.assertDirectoryIsReadable(BASECALLS_DIR);
final List<String> errors = new ArrayList<>();
for (final Integer lane : LANES) {
if (lane < 1) {
errors.add(
"LANES must be greater than or equal to 1. LANES passed in " + StringUtil.join(", ", LANES));
break;
}
}
if (errors.isEmpty()) {
return null;
} else {
return errors.toArray(new String[errors.size()]);
}
}
开发者ID:broadinstitute,项目名称:picard,代码行数:20,代码来源:CheckIlluminaDirectory.java
示例6: testDebugOption
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
/**
* makes sure debug files are created properly
*/
@Test(dataProvider = "dataTestDebugOption")
public void testDebugOption(Boolean writeDebugReads, boolean isDebugFileExpected) throws Exception {
// input as SAM file
final File inputSam = new File("testdata/picard/sam/aligned.sam");
final File javascriptFile = new File("testdata/picard/sam/FilterSamReads/filterOddStarts.js");
FilterSamReads filterTest = setupProgram(javascriptFile, inputSam, FilterSamReads.Filter.includeJavascript, writeDebugReads);
Assert.assertEquals(filterTest.doWork(), 0);
final File inputReadsFile = new File(filterTest.OUTPUT.getParentFile(), IOUtil.basename(filterTest.INPUT) + ".reads");
Assert.assertEquals(inputReadsFile.exists(), isDebugFileExpected);
final File outputReadsFile = new File(filterTest.OUTPUT.getParentFile(), IOUtil.basename(filterTest.OUTPUT) + ".reads");
outputReadsFile.deleteOnExit();
Assert.assertEquals(outputReadsFile.exists(), isDebugFileExpected);
// We have to clean up the debug files after each test is run to make sure a clean state is preserved in between tests
// This mostly affects the input *.reads file because it will always be called "aligned.reads" and will cause future
// tests to fail if it sticks around and we dont expect it to be written
Files.deleteIfExists(inputReadsFile.toPath());
}
开发者ID:broadinstitute,项目名称:picard,代码行数:25,代码来源:FilterSamReadsTest.java
示例7: TileIndex
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
TileIndex(final File tileIndexFile) {
try {
this.tileIndexFile = tileIndexFile;
final InputStream is = IOUtil.maybeBufferInputStream(new FileInputStream(tileIndexFile));
final ByteBuffer buf = ByteBuffer.allocate(8);
buf.order(ByteOrder.LITTLE_ENDIAN);
int absoluteRecordIndex = 0;
int numTiles = 0;
while (readTileIndexRecord(buf.array(), buf.capacity(), is)) {
buf.rewind();
buf.limit(buf.capacity());
final int tile = buf.getInt();
// Note: not handling unsigned ints > 2^31, but could if one of these exceptions is thrown.
if (tile < 0) throw new PicardException("Tile number too large in " + tileIndexFile.getAbsolutePath());
final int numClusters = buf.getInt();
if (numClusters < 0) throw new PicardException("Cluster size too large in " + tileIndexFile.getAbsolutePath());
tiles.add(new TileIndexRecord(tile, numClusters, absoluteRecordIndex, numTiles++));
absoluteRecordIndex += numClusters;
}
CloserUtil.close(is);
} catch (final IOException e) {
throw new PicardException("Problem reading " + tileIndexFile.getAbsolutePath(), e);
}
}
开发者ID:broadinstitute,项目名称:picard,代码行数:25,代码来源:TileIndex.java
示例8: testWriteLaneMetrics
import htsjdk.samtools.util.IOUtil; //导入依赖的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9: withIntervals
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
@Test
public void withIntervals() throws IOException {
final File input = new File(REFERENCE);
final File outfile = File.createTempFile("nonNcount", ".txt");
final File intervals = new File("testdata/picard/reference/test.intervals");
outfile.deleteOnExit();
final String[] args = new String[] {
"INPUT=" + input.getAbsolutePath(),
"OUTPUT=" + outfile.getAbsolutePath(),
"INTERVALS=" + intervals.getAbsolutePath()
};
Assert.assertEquals(new NonNFastaSize().instanceMain(args), 0);
final BufferedReader reader = IOUtil.openFileForBufferedReading(outfile);
final String count = reader.readLine();
try {
Assert.assertEquals(Long.parseLong(count), 53);
} catch (Exception e) {
System.err.println("Failed to read in count because of error: " + e.getMessage());
}
}
开发者ID:broadinstitute,项目名称:picard,代码行数:23,代码来源:NonNFastaSizeTest.java
示例10: testCollectIlluminaLaneMetrics
import htsjdk.samtools.util.IOUtil; //导入依赖的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11: fakeFiles
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
@Override
public List<String> fakeFiles(final List<Integer> expectedTiles, final int[] expectedCycles,
final IlluminaFileUtil.SupportedIlluminaFormat format) {
//we need to fake a bci file for the tile index
final BciFileFaker bciFileFaker = new BciFileFaker();
try {
bciFileFaker.fakeBciFile(bci, expectedTiles);
tileIndex = new TileIndex(bci);
faker.fakeFile(base, expectedTiles, lane, extension);
final File[] filesMatchingRegexp = IOUtil.getFilesMatchingRegexp(base, matchPattern);
if (filesMatchingRegexp == null || filesMatchingRegexp.length == 0) {
dataFile = null;
} else if (filesMatchingRegexp.length == 1) {
dataFile = filesMatchingRegexp[0];
} else {
throw new PicardException("More than one filter file found in " + base.getAbsolutePath());
}
} catch (final IOException e) {
return Collections.singletonList("Could not create tile index file: " + bci.getAbsolutePath());
}
return tileIndex.verify(expectedTiles);
}
开发者ID:broadinstitute,项目名称:picard,代码行数:23,代码来源:MultiTileFileUtil.java
示例12: renderPhasingMetricsFilesFromBasecallingDirectory
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
public static Map<Integer, File> renderPhasingMetricsFilesFromBasecallingDirectory(File illuminaRunDirectory) {
File[] cycleDirs = IOUtil.getFilesMatchingRegexp(new File(illuminaRunDirectory, INTEROP_SUBDIRECTORY_NAME),
IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN);
Map<Integer, File> phasingMetrics = new HashMap<>();
Arrays.asList(cycleDirs)
.forEach(cycleDir -> {
File[] filesMatchingRegexp = IOUtil.getFilesMatchingRegexp(
cycleDir, "EmpiricalPhasingMetricsOut.bin");
if (filesMatchingRegexp.length > 0) {
phasingMetrics.put(PerTilePerCycleFileUtil.getCycleFromDir(cycleDir),
filesMatchingRegexp[0]);
}
});
return phasingMetrics;
}
开发者ID:broadinstitute,项目名称:picard,代码行数:17,代码来源:TileMetricsUtil.java
示例13: hasCbcls
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
public static boolean hasCbcls(final File basecallDir, final int lane) {
final File laneDir = new File(basecallDir, IlluminaFileUtil.longLaneStr(lane));
final File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN);
// Either the lane or the cycle directory do not exist!
if (cycleDirs == null) {
return false;
}
//CBCLs
final List<File> cbcls = new ArrayList<>();
Arrays.asList(cycleDirs)
.forEach(cycleDir -> cbcls.addAll(
Arrays.asList(IOUtil.getFilesMatchingRegexp(
cycleDir, "^" + IlluminaFileUtil.longLaneStr(lane) + "_(\\d{1,5}).cbcl$"))));
return cbcls.size() > 0;
}
开发者ID:broadinstitute,项目名称:picard,代码行数:19,代码来源:IlluminaFileUtil.java
示例14: getPerTilePerCycleFiles
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
/**
* For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through
* all the files for these tiles in expectedBase
* Side Effect: Assigns numCycles
*
* @return A CycleIlluminaFileMap with the listed (or all) tiles for at least expectedCycles number of cycles(or total available
* cycles if expectedCycles is null)
*/
protected CycleIlluminaFileMap getPerTilePerCycleFiles() {
final CycleIlluminaFileMap cycledMap = new CycleIlluminaFileMap();
final File laneDir = base;
final File[] tempCycleDirs;
tempCycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN);
if (tempCycleDirs == null || tempCycleDirs.length == 0) {
return cycledMap;
}
for (final File tempCycleDir : tempCycleDirs) {
detectedCycles.add(getCycleFromDir(tempCycleDir));
}
final Set<Integer> uniqueTiles = new HashSet<Integer>();
for (final File cycleDir : tempCycleDirs) {
final IlluminaFileMap fileMap = getTiledFiles(cycleDir, matchPattern);
uniqueTiles.addAll(fileMap.keySet());
cycledMap.put(getCycleFromDir(cycleDir), fileMap);
}
this.tiles = new ArrayList<>(uniqueTiles);
return cycledMap;
}
开发者ID:broadinstitute,项目名称:picard,代码行数:34,代码来源:PerTilePerCycleFileUtil.java
示例15: buildSamFileWriter
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
/**
* Build a SamFileWriter that will write its contents to the output file.
*
* @param output The file to which to write
* @param sampleAlias The sample alias set in the read group header
* @param libraryName The name of the library to which this read group belongs
* @param headerParameters Header parameters that will be added to the RG header for this SamFile
* @return A SAMFileWriter
*/
private SAMFileWriterWrapper buildSamFileWriter(final File output, final String sampleAlias,
final String libraryName, final Map<String, String> headerParameters,
final boolean presorted) {
IOUtil.assertFileIsWritable(output);
final SAMReadGroupRecord rg = new SAMReadGroupRecord(READ_GROUP_ID);
rg.setSample(sampleAlias);
if (libraryName != null) rg.setLibrary(libraryName);
for (final Map.Entry<String, String> tagNameToValue : headerParameters.entrySet()) {
if (tagNameToValue.getValue() != null) {
rg.setAttribute(tagNameToValue.getKey(), tagNameToValue.getValue());
}
}
final SAMFileHeader header = new SAMFileHeader();
header.setSortOrder(SAMFileHeader.SortOrder.queryname);
header.addReadGroup(rg);
return new SAMFileWriterWrapper(new SAMFileWriterFactory().makeSAMOrBAMWriter(header, presorted, output));
}
开发者ID:broadinstitute,项目名称:picard,代码行数:30,代码来源:IlluminaBasecallsToSam.java
示例16: doWork
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
if (reader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
throw new SAMException("Input must be coordinate-sorted for this program to run. Found: " + reader.getFileHeader().getSortOrder());
}
final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT);
writer.setProgressLogger(
new ProgressLogger(log, (int) 1e7, "Wrote", "records"));
final ReferenceSequenceFileWalker refSeqWalker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
StreamSupport.stream(reader.spliterator(), false)
.peek(rec -> fixRecord(rec, refSeqWalker))
.forEach(writer::addAlignment);
CloserUtil.close(reader);
writer.close();
return 0;
}
开发者ID:broadinstitute,项目名称:picard,代码行数:23,代码来源:SetNmMdAndUqTags.java
示例17: testNonBarcodedWithTagPerMolecularIndexDual
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
@Test
public void testNonBarcodedWithTagPerMolecularIndexDual() throws Exception {
final File outputBam = File.createTempFile("nonBarcodedWithDualMI.", ".sam");
outputBam.deleteOnExit();
final int lane = 1;
Assert.assertEquals(runPicardCommandLine(new String[]{
"BASECALLS_DIR=" + BASECALLS_DIR,
"LANE=" + lane,
"READ_STRUCTURE=25S4M4M25T",
"OUTPUT=" + outputBam,
"RUN_BARCODE=HiMom",
"SAMPLE_ALIAS=HiDad",
"LIBRARY_NAME=Hello, World",
"TAG_PER_MOLECULAR_INDEX=ZA",
"TAG_PER_MOLECULAR_INDEX=ZB"
}), 0);
IOUtil.assertFilesEqual(outputBam, new File(TEST_DATA_DIR, "nonBarcodedWithTagPerMolecularIndex4M4M.sam"));
}
开发者ID:broadinstitute,项目名称:picard,代码行数:21,代码来源:IlluminaBasecallsToSamTest.java
示例18: testMissingPhasingValuesStrict
import htsjdk.samtools.util.IOUtil; //导入依赖的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19: testContaminationDetection
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
@Test(dataProvider = "UnmappedReadStrategies")
public void testContaminationDetection(final AbstractAlignmentMerger.UnmappingReadStrategy strategy, final String basename) throws IOException {
final File unmappedSam = new File(TEST_DATA_DIR, "contam.unmapped.sam");
final File alignedSam = new File(TEST_DATA_DIR, "contam.aligned.sam");
final File expectedSam = new File(TEST_DATA_DIR, basename);
final File refFasta = new File(TEST_DATA_DIR, "cliptest.fasta");
final File mergedSam = File.createTempFile("merged", ".sam");
mergedSam.deleteOnExit();
doMergeAlignment(unmappedSam, Collections.singletonList(alignedSam),
null, null, null, null,
false, true, false, 1,
"0", "1.0", "align!", "myAligner",
true, refFasta, mergedSam,
null, null, null, null, true, SAMFileHeader.SortOrder.coordinate, strategy);
assertSamValid(mergedSam);
IOUtil.assertFilesEqual(expectedSam, mergedSam);
}
开发者ID:broadinstitute,项目名称:picard,代码行数:20,代码来源:MergeBamAlignmentTest.java
示例20: runTool
import htsjdk.samtools.util.IOUtil; //导入依赖的package包/类
@Override
protected void runTool(final JavaSparkContext ctx) {
//TODO remove me when https://github.com/broadinstitute/gatk/issues/4274 and https://github.com/broadinstitute/gatk/issues/4303 are fixed
if(hcArgs.emitReferenceConfidence == ReferenceConfidenceMode.GVCF
&& (AbstractFeatureReader.hasBlockCompressedExtension(output) || output.endsWith(IOUtil.BCF_FILE_EXTENSION))) {
throw new UserException.UnimplementedFeature("It is currently not possible to write a compressed g.vcf or g.bcf from HaplotypeCallerSpark. " +
"See https://github.com/broadinstitute/gatk/issues/4274 and https://github.com/broadinstitute/gatk/issues/4303 for more details.");
}
logger.info("********************************************************************************");
logger.info("The output of this tool DOES NOT match the output of HaplotypeCaller. ");
logger.info("It is under development and should not be used for production work. ");
logger.info("For evaluation only.");
logger.info("Use the non-spark HaplotypeCaller if you care about the results. ");
logger.info("********************************************************************************");
final List<SimpleInterval> intervals = hasIntervals() ? getIntervals() : IntervalUtils.getAllIntervalsForReference(getHeaderForReads().getSequenceDictionary());
callVariantsWithHaplotypeCallerAndWriteOutput(ctx, getReads(), getHeaderForReads(), getReference(), intervals, hcArgs, shardingArgs, numReducers, output);
}
开发者ID:broadinstitute,项目名称:gatk,代码行数:19,代码来源:HaplotypeCallerSpark.java
注:本文中的htsjdk.samtools.util.IOUtil类示例整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
请发表评论