Java IOUtil.assertDirectoryIsWritable方法代码示例

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Override
public void onTraversalStart() {
    IOUtil.assertDirectoryIsWritable(OUTPUT_DIRECTORY);
    if ( readArguments.getReadFiles().size() != 1 ) {
        throw new UserException("This tool only accepts a single SAM/BAM/CRAM as input");
    }

    if (SAMPLE) {
        splitters.add(new SampleNameSplitter());
    }
    if (READ_GROUP) {
        splitters.add(new ReadGroupIdSplitter());
    }
    if (LIBRARY_NAME) {
        splitters.add(new LibraryNameSplitter());
    }
    outs = createWriters(splitters);
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
static void assertWritable(final File output, final boolean outputByReadGroup) {
    if (outputByReadGroup) {
        if (output != null) {
            IOUtil.assertDirectoryIsWritable(output);
        }
    } else {
        IOUtil.assertFileIsWritable(output);
    }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Override
protected int doWork() {
    ///////////////////////////////////////////////////////////////////////
    // Test and then load up the inputs
    ///////////////////////////////////////////////////////////////////////
    final boolean outputVcfs = VCF_DIR != null;
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsReadable(TRIOS);
    IOUtil.assertFileIsWritable(OUTPUT);
    if (outputVcfs) IOUtil.assertDirectoryIsWritable(VCF_DIR);

    LOG.info("Loading and filtering trios.");

    final MendelianViolationDetector.Result result =
            VariantProcessor.Builder
                    .generatingAccumulatorsBy(this::buildDetector)
                    .withInput(INPUT)
                    .combiningResultsBy(MendelianViolationDetector.Result::merge)
                    .multithreadingBy(THREAD_COUNT)
                    .build()
                    .process();

    // Write out the metrics!
    final MetricsFile<MendelianViolationMetrics, ?> metricsFile = getMetricsFile();
    for (final MendelianViolationMetrics m : result.metrics()) {
        m.calculateDerivedFields();
        metricsFile.addMetric(m);
    }

    metricsFile.write(OUTPUT);
    writeAllViolations(result);

    return 0;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@SuppressWarnings("unchecked")
public IndexWriteBean(OptionSet options) {
	super();
	String[] requiredOPT = {"path"};
	VannoUtils.checkMissing(options, requiredOPT);
       
       String path = (String) options.valueOf("path");
       IOUtil.assertInputIsValid(path);
       this.path = path;
       
       if(options.has("f")) {
       	format = VannoUtils.parseIndexFileFormat((String)options.valueOf("f"));
       } else {
       	 File tbiIndex = new File(path + TabixUtils.STANDARD_INDEX_EXTENSION);
       	 if(tbiIndex.exists()) {
           	TbiIndex index  = new TbiIndex(tbiIndex.getAbsolutePath());
           	format = index.getFormatWithRef();
            } 
       }
       if(format == null) throw new IllegalArgumentException("File format is missing, format can be " + ErrorMsg.INDEX_FILE_FORMAT_CMD);
       
       if(options.has("columns") && format.flag != FormatWithRef.VCF_FORMAT) {
       	format = VannoUtils.updateFormat(path, format, (List<String>)options.valuesOf("columns"));
       }
	format.checkOverlap();

	if(options.has("comment")) {
		String comment = (String)options.valueOf("comment");
		if(comment.length() > 1) throw new IllegalArgumentException("metaCharacter should be a char, not " + comment);
		format.tbiFormat.metaCharacter = comment.charAt(0);
	} else {
		format.tbiFormat.metaCharacter = '#';
	}
	if(options.has("skip")) {
		format.tbiFormat.numHeaderLinesToSkip = (Integer)options.valueOf("skip");
	} else {
		format.tbiFormat.numHeaderLinesToSkip = 0;
	}
		
	type = INDEXTYPE.ALL;
       if(options.has("t")) type = VannoUtils.checkWriteIndexType((String)options.valueOf("t"));
       
       String pathDir = null;
       if(options.has("o")) {
       	pathDir = (String)options.valueOf("o");
   		IOUtil.assertDirectoryIsWritable(new File(pathDir));
       }
       
       if(pathDir == null) {
       	outputPathPlus = path + BinIndexWriter.PLUS_EXTENSION;
       	outputPathPlusIndex = path + BinIndexWriter.PLUS_INDEX_EXTENSION;
       } else {
       	if(type == INDEXTYPE.PLUS_INDEX) {
       		outputPathPlus = path + BinIndexWriter.PLUS_EXTENSION;
       		IOUtil.assertInputIsValid(outputPathPlus);
       	} else {
       		outputPathPlus = pathDir + new File(path).getName() + BinIndexWriter.PLUS_EXTENSION;
       	}
       	
       	outputPathPlusIndex = pathDir + new File(path).getName() + BinIndexWriter.PLUS_INDEX_EXTENSION;
       }
}