import htsjdk.tribble.FeatureCodecHeader; //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.FeatureCodecHeader; //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.FeatureCodecHeader; //导入依赖的package包/类
/**
 * @param inputFile The file from which to read. Stream for reading is opened on construction.
 * @param codec feature codec, of features, that iterator should handle
 */
public FeatureIterator(final File inputFile, final FeatureCodec<T, S> codec) {
    this.codec = codec;
    this.inputFile = inputFile;
    final FeatureCodecHeader header = readHeader();
    source = (S) codec.makeIndexableSourceFromStream(initStream(inputFile, header.getHeaderEnd()));
    readNextFeature();
}
 

import htsjdk.tribble.FeatureCodecHeader; //导入依赖的package包/类
/**
 * Some codecs,  e.g. VCF files,  need the header to decode features.  This is a rather poor design,
 * the internal header is set as a side-affect of reading it, but we have to live with it for now.
 */
private FeatureCodecHeader readHeader() {
    try {
        final S sourceFromStream = this.codec.makeSourceFromStream(initStream(inputFile, 0));
        final FeatureCodecHeader header = this.codec.readHeader(sourceFromStream);
        codec.close(sourceFromStream);
        return header;
    } catch (IOException e) {
        LOGGER.error(MessageHelper.getMessage(MessagesConstants.ERROR_FILE_HEADER_READING), e);
        throw new TribbleException.InvalidHeader(e.getMessage());
    }
}
 

import htsjdk.tribble.FeatureCodecHeader; //导入依赖的package包/类
/**
 * @param inputFile The file from which to read. Stream for reading is opened on construction.
 * @param codec
 */
public FeatureIterator(final File inputFile, final FeatureCodec<F, S> codec) {
    this.codec = codec;
    this.inputFile = inputFile;
    final FeatureCodecHeader header = readHeader();
    source =
            (S) makeIndexableSourceFromStream(initStream(inputFile, header.getHeaderEnd()));
    readNextFeature();
}
 

import htsjdk.tribble.FeatureCodecHeader; //导入依赖的package包/类
/**
 * Some codecs,  e.g. VCF files,  need the header to decode features.  This is a rather poor design,
 * the internal header is set as a side-affect of reading it, but we have to live with it for now.
 */
private FeatureCodecHeader readHeader() {
    try {
        final S headerSource = this.codec.makeSourceFromStream(initStream(inputFile, 0));
        final FeatureCodecHeader header = this.codec.readHeader(headerSource);
        codec.close(headerSource);
        return header;
    } catch (final IOException e) {
        throw new IndexException(e.getMessage(), e);
    }
}
 

import htsjdk.tribble.FeatureCodecHeader; //导入依赖的package包/类
@Override
public FeatureCodecHeader readHeader(final B b) throws IOException {
    if (delegatee == null) {
        throw new IllegalStateException("this codec cannot be used without a delegatee.");
    }
    return delegatee.readHeader(b);
}
 

import htsjdk.tribble.FeatureCodecHeader; //导入依赖的package包/类
@Override
	public int run(String[] args) throws Exception {
		BioJob job = BioJob.getInstance();
		Configuration conf = job.getConfiguration();
		conf.setBoolean(GaeaVCFOutputFormat.HEADER_MODIFY, true);
		
		String[] remainArgs = remainArgs(args, conf);
		
		options = new VCFQualityControlOptions();
		options.parse(remainArgs);
		options.setHadoopConf(remainArgs, conf);
		
		//merge header
		vcfHeaders = new MultipleVCFHeader();
		vcfHeaders.mergeHeader(new Path(options.getInputs()), options.getOutputPath(), job, false);
				
		if(options.isRecal()) {
//			vqsr
			job.setJobName("Gaea variant quality score recalibration");
			job.setJarByClass(VCFQualityControl.class);
			job.setMapperClass(VariantRecalibrationMapper.class);
			job.setReducerClass(VariantRecalibrationReducer.class);
			job.setOutputKeyValue(IntWritable.class, Text.class, 
					NullWritable.class, VariantContextWritable.class);
			job.setNumReduceTasks(vcfHeaders.getFileNum());
			
			FileInputFormat.addInputPaths(job, options.getInputs());
			job.setInputFormatClass(VCFMultipleInputFormat.class);
	
			Path statistics = new Path(options.getOutputPath() + "/tmp");
			//job.setOutputFormatClass(VariantRecalibrationOutputFormat.class);
			job.setOutputFormatClass(GaeaVCFOutputFormat.class);
			FileOutputFormat.setOutputPath(job, statistics);
			
			return job.waitForCompletion(true) ? 0 : 1;
		} else {
//			hard filter
			HardFilter fe = new HardFilter(options.getFilterName(), options.getSnpFilter(), options.getIndelFilter());
			for(Path vcfPath : options.getInputFiles()) {
				AsciiLineReaderIterator iterator = new AsciiLineReaderIterator(new AsciiLineReader(HdfsFileManager.getInputStream(vcfPath, conf)));
				VCFCodec codec = new VCFCodec();
				VCFHeader vHeader = (VCFHeader)(((FeatureCodecHeader)codec.readHeader(iterator)).getHeaderValue());
				String output = options.getOutputPath() + vcfPath.toString();
				for(VCFHeaderLine headerLine : fe.filterHeaders())
					vHeader.addMetaDataLine(headerLine);
				
				VCFHdfsWriter writer = new VCFHdfsWriter(output, false, false, conf);
				writer.writeHeader(vHeader);
				
				ReportDatum report = null;
				while(iterator.hasNext()){
					VariantContext vc = codec.decode(iterator.next());
					vc = fe.filter(vc);
					ReportDatum datum = new ReportDatum.Builder(vc).isSnp().isIndel().isTransition().build();
					if(report == null)
						report = datum;
					else
						report.combine(datum);
					writer.add(vc);
				}
			}
			return 1;
		}
	}
 

import htsjdk.tribble.FeatureCodecHeader; //导入依赖的package包/类
@Override
public FeatureCodecHeader readHeader(PositionalBufferedStream stream) throws IOException {
    return this.wrappedCodec.readHeader(stream);
}
 

import htsjdk.tribble.FeatureCodecHeader; //导入依赖的package包/类
@Override
public FeatureCodecHeader readHeader(EmblTableIterator o) throws IOException {
    return null;
}
 

import htsjdk.tribble.FeatureCodecHeader; //导入依赖的package包/类
@Override
public FeatureCodecHeader readHeader(final LineIterator lineIterator) throws IOException {
    return new FeatureCodecHeader(readActualHeader(lineIterator), FeatureCodecHeader.NO_HEADER_END);
}