Java IOUtil.assertFileIsReadable方法代码示例

import htsjdk.samtools.util.IOUtil; //导入方法依赖的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;
	}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的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;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    if(OUTPUT != null) IOUtil.assertFileIsWritable(OUTPUT);

    final MetricsFile<CrosscheckMetric, ?> metricsFile = getMetricsFile();

    try {
        metricsFile.read(new FileReader(INPUT));
    } catch (FileNotFoundException e) {
        e.printStackTrace();
        return 1;
    }

    clusterMetrics(metricsFile.getMetrics()).write(OUTPUT);

    return 0;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);

    IntervalList intervals = IntervalList.fromFile(INPUT);
    if (SORT) intervals = intervals.sorted();

    try {
        final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT);
        for (final Interval i : intervals) {
            final String strand = i.isNegativeStrand() ? "-" : "+";
            final List<?> fields = CollectionUtil.makeList(i.getContig(), i.getStart()-1, i.getEnd(), i.getName(), SCORE, strand);
            out.append(fields.stream().map(String::valueOf).collect(Collectors.joining("\t")));
            out.newLine();
        }

        out.close();
    }
    catch (IOException ioe) {
        throw new RuntimeIOException(ioe);
    }

    return 0;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);

    if (INPUT.getAbsolutePath().endsWith(".sam")) {
        throw new PicardException("SAM files are not supported");
    }

    final SAMFileHeader samFileHeader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).getFileHeader(INPUT);
    for (final String comment : COMMENT) {
        if (comment.contains("\n")) {
            throw new PicardException("Comments can not contain a new line");
        }
        samFileHeader.addComment(comment);
    }

    BamFileIoUtils.reheaderBamFile(samFileHeader, INPUT, OUTPUT, CREATE_MD5_FILE, CREATE_INDEX);

    return 0;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Override protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    try {
        final FileTermination term = BlockCompressedInputStream.checkTermination(INPUT);
        System.err.println(term.name());
        if (term == FileTermination.DEFECTIVE) {
            return 100;
        }
        else {
            return 0;
        }
    }
    catch (IOException ioe) {
        throw new PicardException("Exception reading terminator block of file: " + INPUT.getAbsolutePath());
    }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
private Map<String, Map<String, MatePair>> createPUPairsMap(final File samFile) throws IOException {
    IOUtil.assertFileIsReadable(samFile);
    final SamReader reader = SamReaderFactory.makeDefault().open(samFile);
    final Map<String, Map<String, MatePair>> map = new LinkedHashMap<String, Map<String,MatePair>>();

    Map<String,MatePair> curFileMap;
    for (final SAMRecord record : reader ) {
        final String platformUnit = record.getReadGroup().getPlatformUnit();
        curFileMap = map.get(platformUnit);
        if(curFileMap == null)
        {
            curFileMap = new LinkedHashMap<String, MatePair>();
            map.put(platformUnit, curFileMap);
        }

        MatePair mpair = curFileMap.get(record.getReadName());
        if (mpair == null) {
             mpair = new MatePair();
             curFileMap.put(record.getReadName(), mpair);
        }
        mpair.add(record);
    }
    reader.close();
    return map;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@SuppressWarnings("resource")
public static InputStream openFileForReading(File file) throws IOException
	{
	IOUtil.assertFileIsReadable(file);
	InputStream in= new FileInputStream(file);
	if(file.getName().endsWith(".gz") || file.getName().endsWith(".bgz"))
		{
		in=tryBGZIP(in);
		}
	return in;
	}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的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<String> unrollFiles(java.util.Collection<String> inputs)
	{
	LinkedHashSet<String> vcfFiles= new LinkedHashSet<>(inputs.size()+1);
	for(String file : inputs)
		{
		if(file.isEmpty())
			{
			//ignore
			}
		else if(IOUtil.isUrl(file))
			{
			vcfFiles.add(file);
			}
		else if(file.endsWith(".list"))
			{
			File f = new File(file);
			IOUtil.assertFileIsReadable(f);
			 for (final String s : IOUtil.readLines(f))
			 	{
				if (s.endsWith("#")) continue;
				if (s.trim().isEmpty()) continue;
				vcfFiles.add(s);
				}
			}
		else
			{
			vcfFiles.add(file);
			}
		
		}
	return vcfFiles;
	}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
private static void checkFactoryVars(final int headerSize, final File binaryFile) {
    IOUtil.assertFileIsReadable(binaryFile);

    if(headerSize < 0) {
        throw new PicardException("Header size cannot be negative.  HeaderSize(" + headerSize + ") for file " + binaryFile.getAbsolutePath());
    }

    if(headerSize > binaryFile.length()) {
        throw new PicardException("Header size(" + headerSize + ") is greater than file size(" + binaryFile.length() + ") for file " + binaryFile.getAbsolutePath());
    }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
private void assertIoFiles(final File summaryFile, final File detailsFile, final File plotsFile) {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
    IOUtil.assertFileIsWritable(summaryFile);
    IOUtil.assertFileIsWritable(detailsFile);
    IOUtil.assertFileIsWritable(plotsFile);
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
private int getReadCounts(final Path tempDirectory, final String baseName, final String fileName) {
    final File path = tempDirectory.resolve(fileName).toFile();
    IOUtil.assertFileIsReadable(path);
    final SamReader in = SamReaderFactory.makeDefault().referenceSequence(new File(getTestDataDir(), getReferenceSequenceName(baseName))).open(path);
    int count = 0;
    for (@SuppressWarnings("unused") final SAMRecord rec : in) {
        count++;
    }
    CloserUtil.close(in);
    return count;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
/**
 * Main method for the program.  Checks that input file is present and
 * readable, then iterates through the index printing meta data to stdout.
 */
protected int doWork() {

    if (INPUT.getName().endsWith(BAMIndex.BAMIndexSuffix))
           log.warn("INPUT should be the BAM file name, not its index file");
    IOUtil.assertFileIsReadable(INPUT);
    BAMIndexMetaData.printIndexStats(INPUT);

    return 0;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
/**
 * Do the work after command line has been parsed.
 * RuntimeException may be thrown by this method, and are reported appropriately.
 *
 * @return program exit status.
 */
@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);
    final SamReaderFactory factory = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE);
    if (VALIDATION_STRINGENCY == ValidationStringency.STRICT) {
        factory.validationStringency(ValidationStringency.LENIENT);
    }
    final SamReader reader = factory.open(INPUT);
    final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT);
    final CloseableIterator<SAMRecord> it = reader.iterator();
    final ProgressLogger progress = new ProgressLogger(Log.getInstance(CleanSam.class));

    // If the read (or its mate) maps off the end of the alignment, clip it
    while (it.hasNext()) {
        final SAMRecord rec = it.next();

        // If the read (or its mate) maps off the end of the alignment, clip it
        AbstractAlignmentMerger.createNewCigarsIfMapsOffEndOfReference(rec);

        // check the read's mapping quality
        if (rec.getReadUnmappedFlag() && 0 != rec.getMappingQuality()) {
            rec.setMappingQuality(0);
        }

        writer.addAlignment(rec);
        progress.record(rec);
    }

    writer.close();
    it.close();
    CloserUtil.close(reader);
    return 0;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
protected String[] customCommandLineValidation() {
    IOUtil.assertFileIsReadable(INPUT);

    boolean isBamOrSamFile = isBamOrSamFile(INPUT);
    if (!isBamOrSamFile && IGNORE_READ_GROUPS) {
        return new String[]{"The parameter IGNORE_READ_GROUPS can only be used with BAM/SAM inputs."};
    }
    if (isBamOrSamFile && OBSERVED_SAMPLE_ALIAS != null) {
        return new String[]{"The parameter OBSERVED_SAMPLE_ALIAS can only be used with a VCF input."};
    }
    return super.customCommandLineValidation();
}