import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) {
    String nextLine;

    try {
        nextLine = reader.readLine();
        while (nextLine.startsWith("#")) {
            writer.println(nextLine);
            nextLine = reader.readLine();
        }
    } catch (IOException e) {
        throw new RuntimeIOException(e);
    }

    return nextLine;
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) throws IOException {

    String nextLine = reader.readLine();

    if (nextLine.startsWith("psLayout")) {
        do {
            writer.println(nextLine);
            nextLine = reader.readLine();
        } while (!nextLine.startsWith("-"));
        nextLine = reader.readLine();
    }
    while (nextLine.startsWith("#") ||
            nextLine.startsWith("browser") ||
            nextLine.startsWith("track") ||
            isEmptyLine(nextLine)) {
        writer.println(nextLine);
        nextLine = reader.readLine();
    }

    return nextLine;

}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) {
    try {
        String nextLine = reader.readLine();
        while (nextLine.startsWith("#")) {
            writer.println(nextLine);
            nextLine = reader.readLine();
        }

        return nextLine;
    } catch (IOException e) {
        LOG.error("Error writing header", e);
        return null;
    }


}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
public void readSingleHeader(Path vcfPath, Configuration conf) throws IOException {
	FileSystem fs = vcfPath.getFileSystem(conf);
	if(!fs.exists(vcfPath))
		throw new RuntimeException(vcfPath.toString() + " don't exists.");
	if(!fs.isFile(vcfPath)) {
		throw new RuntimeException(vcfPath.toString() + " is not a file. GaeaSingleVcfHeader parser only support one vcf file.");
	}
	FSDataInputStream in = fs.open(vcfPath);
	AsciiLineReaderIterator it = new AsciiLineReaderIterator(new AsciiLineReader(in));
    VCFCodec codec = new VCFCodec();
    Object header = codec.readHeader(it);
	vcfHeader = (VCFHeader)(((FeatureCodecHeader)header).getHeaderValue());
	sampleNames.addAll(vcfHeader.getGenotypeSamples());
	buildHeaderInfo();
	it.close();
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
/** A VCFHeader is read from the input Path. */
public GaeaVCFRecordWriter(
		Path output, Path input, boolean writeHeader, TaskAttemptContext ctx)
	throws IOException
{
	final AsciiLineReader r = new AsciiLineReader(
		input.getFileSystem(ContextUtil.getConfiguration(ctx)).open(input));

	final Object h = codec.readHeader(new AsciiLineReaderIterator(r));
	if (!(h instanceof VCFHeader))
		throw new IOException("No VCF header found in "+ input);

	r.close();

	init(output, (VCFHeader)h, writeHeader, ctx);
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
/**
 * Validate cytoband file
 *
 * @param reader
 * @param filename
 * @return
 */
public static boolean isValid(AsciiLineReader reader, String filename) {

    if (reader == null) {
        return false;
    }

    try {
        String nextLine;
        while ((nextLine = reader.readLine()) != null) {
            String[] tokens = nextLine.split("\t");
            String chr = tokens[0].trim();
            Cytoband cytoData = new Cytoband(chr);
            parseData(tokens, cytoData);
        }
        return true;

    } catch (Exception e) {
        logger.error("Invalid Cytoband file data : file=" + filename, e);
        return false;
    }
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
public static boolean parsableMAGE_TAB(ResourceLocator file) throws IOException {
    AsciiLineReader reader = null;
    try {
        reader = ParsingUtils.openAsciiReader(file);
        String nextLine = null;

        //skip first row
        reader.readLine();

        //check second row for MAGE_TAB identifiers
        if ((nextLine = reader.readLine()) != null && (nextLine.contains("Reporter REF") ||
                nextLine.contains("Composite Element REF") || nextLine.contains("Term Source REF") ||
                nextLine.contains("CompositeElement REF") || nextLine.contains("TermSource REF") ||
                nextLine.contains("Coordinates REF"))) {
            return true;
        }
    } finally {
        if (reader != null) {
            reader.close();
        }
    }

    return false;
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
/**
 * Load attributes from an ascii file in "Sample Info" format.
 */
public void loadSampleInfo(ResourceLocator locator) {
    AsciiLineReader reader = null;
    try {
        reader = ParsingUtils.openAsciiReader(locator);

        loadSampleTable(reader, locator.getPath());

        loadedResources.add(locator);

        if (!Globals.isHeadless()) {
            IGV.getInstance().resetOverlayTracks();
            IGV.getInstance().doRefresh();
        }

    } catch (IOException ex) {
        log.error("Error loading attribute file", ex);
        throw new DataLoadException("Error reading attribute file", locator.getPath());
    } finally {
        if (reader != null) {
            reader.close();

        }
        firePropertyChange(this, ATTRIBUTES_LOADED_PROPERTY, null, null);
    }
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) {
    String nextLine = null;

    try {
        nextLine = reader.readLine();
        while (nextLine.startsWith("#")) {
            writer.println(nextLine);
            nextLine = reader.readLine();
        }
    } catch (IOException e) {
        e.printStackTrace();
    }

    return nextLine;
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) throws IOException {

    String nextLine = reader.readLine();

    if (nextLine.startsWith("psLayout")) {
        do {
            writer.println(nextLine);
            nextLine = reader.readLine();
        } while (!nextLine.startsWith("-"));
        nextLine = reader.readLine();
    }
    // TODO -- check "browser" line syntax,  is it a multi-line directive?
    while (nextLine.startsWith("#") ||
            nextLine.startsWith("browser") ||
            nextLine.startsWith("track") ||
            nextLine.trim().length() == 0) {
        writer.println(nextLine);
        nextLine = reader.readLine();
    }

    return nextLine;


}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) throws IOException {

    String nextLine;
    // TODO -- check "browser" line syntax,  is it a multi-line directive?
    while ((nextLine = reader.readLine()).startsWith("#")) {
        writer.println(nextLine);   // Comments, directives
    }
    writer.println(nextLine);  // Header

    // Contract is to return the first data line!
    nextLine = reader.readLine();

    return nextLine;


}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) {
    try {
        String nextLine = reader.readLine();
        // TODO -- check "browser" line syntax,  is it a multi-line directive?
        while (nextLine.startsWith("#")) {
            writer.println(nextLine);
            nextLine = reader.readLine();
        }

        return nextLine;
    } catch (IOException e) {
        log.error("Error writing header", e);
        return null;
    }


}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
/**
 * Utility method.  Returns true if this looks like a wiggle locator.  The criteria is to scan
 * the first 100 lines looking for a valid "track" line.  According to UCSC documentation
 * track lines must contain a type attribute,  which must be equal to "wiggle_0".
 *
 * @param file
 * @return
 */
public static boolean isWiggle(ResourceLocator file) {
    AsciiLineReader reader = null;
    try {
        reader = ParsingUtils.openAsciiReader(file);
        String nextLine = null;
        int lineNo = 0;
        while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
            if (nextLine.startsWith("track") && nextLine.contains("wiggle_0")) {
                return true;
            }
            if (lineNo++ > 100) {
                break;
            }
        }
    } catch (IOException e) {
        e.printStackTrace();
        return false;
    } finally {
        if (reader != null) {
            reader.close();
        }
    }
    return false;
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
/**
 * Gets the set (no duplicates) of chromosomes from a bed file.
 *
 * @param bedFilePath Path to the bed file.
 *
 * @return The set of chromosomes (no duplicates)
 *
 * @throws FileNotFoundException, IOException
 */
public static Set<String> getChromosomes(String bedFilePath) throws FileNotFoundException, IOException {
    Set<String> chrs = new LinkedHashSet<>();
    File bedFile = FileUtils.getFile(bedFilePath);
    try (InputStream is = new FileInputStream(bedFile);
            AsciiLineReader alr = new AsciiLineReader(is);
            LineIteratorImpl lineIterator = new LineIteratorImpl(alr);) {
        BEDCodec bc = new BEDCodec();
        while (!bc.isDone(lineIterator)) {
            BEDFeature bf = bc.decode(lineIterator);
            if (bf != null) {
                //see https://github.com/samtools/htsjdk/issues/197
                chrs.add(bf.getContig());
            }
        }
    }
    return chrs;
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
/** returns the number of lines in the file that contain a regular expression (decorated with "MV=" and
 * expected to be in an INFO field in a vcf)
 *
 * @param file File to examine
 * @param regex String containing a regular expression to look for in the file
 * @return the number of lines that contain regex
 */
private int grep(final File file, final String regex) {

    int results = 0;
    final Pattern pattern = Pattern.compile(".*"+regex+".*");
    try (final LineIteratorImpl li = new LineIteratorImpl(new AsciiLineReader(IOUtil.openFileForReading(file)))) {

        while (li.hasNext()) {
            final String line = li.next();
            if (pattern.matcher(line).matches()) {
                results++;
            }
        }
    } catch (final IOException e) {
        e.printStackTrace();
    }
    return results;
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
/** A VCFHeader is read from the input Path. */
public VCFRecordWriter(
		Path output, Path input, boolean writeHeader, TaskAttemptContext ctx)
	throws IOException
{
	final AsciiLineReader r = new AsciiLineReader(
		input.getFileSystem(ctx.getConfiguration()).open(input));

	final FeatureCodecHeader h = codec.readHeader(new AsciiLineReaderIterator(r));
	if (h == null || !(h.getHeaderValue() instanceof VCFHeader))
		throw new IOException("No VCF header found in "+ input);

	r.close();

	init(output, (VCFHeader) h.getHeaderValue(), writeHeader, ctx);
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
public LineReader  execute() throws IOException
{
URLConnection connection = new URL(this.getServiceUrl()).openConnection();
connection.setDoOutput(true); 
connection.setRequestProperty("Accept-Charset", this.getCharSet());
connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded;charset=" + this.getCharSet());
if(connection instanceof HttpURLConnection )
        {
        HttpURLConnection httpConnection = (HttpURLConnection)connection;
        httpConnection.setRequestMethod("POST");
        httpConnection.setInstanceFollowRedirects(true);
        }
	
String q="query="+URLEncoder.encode(this.getXmlString(),this.getCharSet());
OutputStream output = null;
try {
     output = connection.getOutputStream();
     output.write(q.getBytes(this.getCharSet()));
     output.flush();
} finally {
     if (output != null) try { output.close(); } catch (IOException logOrIgnore) {logOrIgnore.printStackTrace();}
}
InputStream response = connection.getInputStream();
AsciiLineReader r=new AsciiLineReader(response);
return r;
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
/**
 * @param maxMemory - in megabytes
 * @throws IOException
 *
 */
public void run(int maxMemory) throws IOException {
    try (
            PrintWriter writer = NgbFileUtils.isGzCompressed(outputFile.getName()) ?
                    new PrintWriter(new OutputStreamWriter(new BlockCompressedOutputStream(outputFile), UTF_8)) :
                    new PrintWriter(outputFile, UTF_8);
            AsciiLineReader reader = NgbFileUtils.isGzCompressed(outputFile.getName()) ?
                    new AsciiLineReader(new BlockCompressedInputStream(inputFile)) :
                    new AsciiLineReader(new FileInputStream(inputFile))
    ) {

        SortableRecordCodec codec = new SortableRecordCodec();

        SortingCollection cltn = SortingCollection.newInstance(
                SortableRecord.class, codec, comparator, maxMemory * 1024 * 1024 / ESTIMATED_RECORD_SIZE, tmpDir);

        Parser parser = getParser();

        String firstDataRow = writeHeader(reader, writer);
        if (firstDataRow != null && !firstDataRow.isEmpty()) {
            cltn.add(parser.createRecord(firstDataRow));
        }

        SortableRecord next;
        while ((next = parser.readNextRecord(reader)) != null) {
            cltn.add(next);
        }

        CloseableIterator<SortableRecord> iter = cltn.iterator();
        while (iter.hasNext()) {
            SortableRecord al = iter.next();
            writer.println(al.getText());

        }
        iter.close();
    }
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
private static Index createIndex(InputStream is) throws IOException {
	TabixIndexCreator ctor = new TabixIndexCreator(TabixFormat.VCF);
	VCFCodec codec = new VCFCodec();
	VariantContext lastContext = null;
       VariantContext currentContext;
       final Map<String, VariantContext> visitedChromos = new HashMap<String, VariantContext>();
       AsciiLineReader lineReader = new AsciiLineReader(is);
       AsciiLineReaderIterator iterator = new AsciiLineReaderIterator(lineReader);
       codec.readActualHeader(iterator);
       while (iterator.hasNext()) {
           final long position = iterator.getPosition();
           currentContext = codec.decode(iterator.next());
           checkSorted(lastContext, currentContext);
           //should only visit chromosomes once
           final String curChr = currentContext.getChr();
           final String lastChr = lastContext != null ? lastContext.getChr() : null;
           if(!curChr.equals(lastChr)){
               if(visitedChromos.containsKey(curChr)){
               	throw new RuntimeException("Input file must have contiguous chromosomes.");
               }else{
                   visitedChromos.put(curChr, currentContext);
               }
           }

           ctor.addFeature(currentContext, position);

           lastContext = currentContext;
       }

       iterator.close();
       
       return ctor.finalizeIndex(iterator.getPosition());
}
 

import htsjdk.tribble.readers.AsciiLineReader; //导入依赖的package包/类
@Override
public void seek(long pos){
	this.pos = pos;
	try {
		seekableStream.seek(this.pos);
	} catch (IOException e) {
		// TODO Auto-generated catch block
		throw new RuntimeException(e.toString());
	}
	iterator = new AsciiLineReaderIterator(new AsciiLineReader(seekableStream));
}