Java VCFHeaderVersion.toHeaderVersion方法代码示例

import htsjdk.variant.vcf.VCFHeaderVersion; //导入方法依赖的package包/类
/**
    * Reads all of the header from the provided iterator, but no reads no further.
    * @param lineIterator the line reader to take header lines from
    * @return The parsed header
    */
   @SuppressWarnings("static-access")
@Override
   public Object readActualHeader(final LineIterator lineIterator) {
       final List<String> headerStrings = new ArrayList<String>();

       String line;
       boolean foundHeaderVersion = false;
       while (lineIterator.hasNext()) {
           line = lineIterator.peek();
           lineNo++;
           if (line.startsWith(VCFHeader.METADATA_INDICATOR)) {
               final String[] lineFields = line.substring(2).split("=");
               if (lineFields.length == 2 && VCFHeaderVersion.isFormatString(lineFields[0]) ) {
                   if ( !VCFHeaderVersion.isVersionString(lineFields[1]) )
                       throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version");
                   foundHeaderVersion = true;
                   version = VCFHeaderVersion.toHeaderVersion(lineFields[1]);
                   if ( ! version.isAtLeastAsRecentAs(VCFHeaderVersion.VCF4_0) )
                       throw new TribbleException.InvalidHeader("This codec is strictly for VCFv4; please use the VCF3 codec for " + lineFields[1]);
                   if ( version != VCFHeaderVersion.VCF4_0 && version != VCFHeaderVersion.VCF4_1 && version != VCFHeaderVersion.VCF4_2 )
                       throw new TribbleException.InvalidHeader("This codec is strictly for VCFv4 and does not support " + lineFields[1]);
               }
               headerStrings.add(lineIterator.next());
           }
           else if (line.startsWith(VCFHeader.HEADER_INDICATOR)) {
               if (!foundHeaderVersion) {
                   throw new TribbleException.InvalidHeader("We never saw a header line specifying VCF version");
               }
               headerStrings.add(lineIterator.next());
               super.parseHeaderFromLines(headerStrings, version);
               return this.header;
           }
           else {
               throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file");
           }

       }
       throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file");
   }
 

import htsjdk.variant.vcf.VCFHeaderVersion; //导入方法依赖的package包/类
public static VCFHeaderVersion getVCFHeaderVersion(VCFHeader vcfHeader){
	Iterator<VCFHeaderLine> iter = vcfHeader.getMetaDataInInputOrder().iterator();
	while(iter.hasNext()){
		VCFHeaderLine hl = iter.next();
		if(hl.getKey().equals("fileformat")){
			return VCFHeaderVersion.toHeaderVersion(hl.getValue());
		}
	}
	return null;
}
 

import htsjdk.variant.vcf.VCFHeaderVersion; //导入方法依赖的package包/类
@Override public void setHeader(VCFHeader header) {
	VCFHeaderVersion version = null;

	// Normally AbstractVCFCodec parses the header and thereby sets the
	// version field. It gets used later on so we need to set it.
	for (final VCFHeaderLine line : header.getMetaDataInInputOrder()) {
		if (VCFHeaderVersion.isFormatString(line.getKey())) {
			version = VCFHeaderVersion.toHeaderVersion(line.getValue());
			break;
		}
	}

	codec.setHeaderAndVersion(header, version);
}
 

import htsjdk.variant.vcf.VCFHeaderVersion; //导入方法依赖的package包/类
private static VCFHeader warpHeader(VCFHeader in, Map<String, Long> namesAndLength)
    throws IllegalArgumentException {
  Set<VCFHeaderLine> newLines = new HashSet<>();
  boolean hasSource = false;
  VCFHeaderVersion version = DEFAULT_VCF_VERSION;

  for (VCFHeaderLine line : in.getMetaDataInInputOrder()) {
    if (line.getKey().equals("reference")) {
      newLines.add(new VCFHeaderLine(line.getKey(), ARGS.refTargetFASTA));
    } else if (line.getKey().equals("source")) {
      newLines.add(new VCFHeaderLine(line.getKey(), line.getValue() + "_and_"
          + GENOME_WARP_VERSION));
      hasSource = true;
    } else if (line.getKey().equals("fileformat")) {
      version = VCFHeaderVersion.toHeaderVersion(line.getValue());
      if (version == null) {
        throw new IllegalArgumentException("malformed version: " + line.getValue());
      }
    } else if (line.getKey().equals(VCFConstants.CONTIG_HEADER_KEY)) {
      continue;
    } else {
      newLines.add(line);
    }
  }

  if (!hasSource) {
    newLines.add(new VCFHeaderLine("source", GENOME_WARP_VERSION));
  }

  // Add contigs
  int i = 0;
  for (Map.Entry<String, Long> entry : namesAndLength.entrySet()) {
    String currName = entry.getKey();
    long chrSize = entry.getValue();

    newLines.add(new VCFContigHeaderLine(VCFHeaderLine.toStringEncoding(
        createContigEntry(currName, chrSize, ARGS.targetAssembly, ARGS.species)),
        version, VCFConstants.CONTIG_HEADER_KEY, i++));
  }

  return new VCFHeader(newLines, in.getSampleNamesInOrder());
}