Java IOUtil.assertInputIsValid方法代码示例

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public AbstractVCFParser(final FormatWithRef format, final String path) {
	super(format);
	this.codec = new VCFCodec();

	IOUtil.assertInputIsValid(path);
	readHeaderFiles(new File(path));
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public VCFHeader outVCFHeader() {
	try {
		if(vcfHeaderPath == null) {
			System.out.println("*** Note: Your output format is vcf, you should define header-path for vcf header or we won't output header.");
			return null;
		} else {
			IOUtil.assertInputIsValid(vcfHeaderPath);
			return (VCFHeader)(new VCFCodec()).readActualHeader(new LineIteratorImpl(new File(vcfHeaderPath)));
		}
	} catch (FileNotFoundException e) {
		e.printStackTrace();
	}
	return null;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setQueryFile(String queryFile) {
	IOUtil.assertInputIsValid(queryFile);
	this.queryFile = queryFile;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setFieldsFormat(String fieldsFormat) {
	IOUtil.assertInputIsValid(fieldsFormat);
	this.fieldsFormat = fieldsFormat;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setFieldVcfInfo(String fieldVcfInfo) {
	IOUtil.assertInputIsValid(fieldVcfInfo);
	this.fieldVcfInfo = fieldVcfInfo;
}
 

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;
       }
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setOverlapFile(String overlapFile) {
	IOUtil.assertInputIsValid(overlapFile);
	this.overlapFile = overlapFile;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setHeaderPath(String headerPath) {
	IOUtil.assertInputIsValid(headerPath);
	this.headerPath = headerPath;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setAnnoConfig(String annoConfig) {
	IOUtil.assertInputIsValid(annoConfig);
	this.annoConfig = annoConfig;
}
 

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setDb(String dbPath) {
	IOUtil.assertInputIsValid(dbPath);
	this.db = dbPath;
}
 

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

    final SamReader in = SamReaderFactory.makeDefault()
        .referenceSequence(REFERENCE_SEQUENCE)
        .open(SamInputResource.of(INPUT));

    // create the read-group we'll be using
    final SAMReadGroupRecord rg = new SAMReadGroupRecord(RGID);
    rg.setLibrary(RGLB);
    rg.setPlatform(RGPL);
    rg.setSample(RGSM);
    rg.setPlatformUnit(RGPU);
    if (RGCN != null) rg.setSequencingCenter(RGCN);
    if (RGDS != null) rg.setDescription(RGDS);
    if (RGDT != null) rg.setRunDate(RGDT);
    if (RGPI != null) rg.setPredictedMedianInsertSize(RGPI);
    if (RGPG != null) rg.setProgramGroup(RGPG);
    if (RGPM != null) rg.setPlatformModel(RGPM);
    if (RGKS != null) rg.setKeySequence(RGKS);
    if (RGFO != null) rg.setFlowOrder(RGFO);

    log.info(String.format("Created read-group ID=%s PL=%s LB=%s SM=%s%n", rg.getId(), rg.getPlatform(), rg.getLibrary(), rg.getSample()));

    // create the new header and output file
    final SAMFileHeader inHeader = in.getFileHeader();
    final SAMFileHeader outHeader = inHeader.clone();
    outHeader.setReadGroups(Collections.singletonList(rg));
    if (SORT_ORDER != null) outHeader.setSortOrder(SORT_ORDER);

    final SAMFileWriter outWriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader,
            outHeader.getSortOrder() == inHeader.getSortOrder(),
            OUTPUT);

    final ProgressLogger progress = new ProgressLogger(log);
    for (final SAMRecord read : in) {
        read.setAttribute(SAMTag.RG.name(), RGID);
        outWriter.addAlignment(read);
        progress.record(read);
    }

    // cleanup
    CloserUtil.close(in);
    outWriter.close();
    return 0;
}