Class VcfReader

src/main/java/com/rtg/vcf/VcfReader.java:48–183

Reads a .vcf input stream and converts it into VCF records.

 * Reads a <code>.vcf</code> input stream and converts it into VCF records.
 */
public class VcfReader implements VcfIterator {

  private final VcfParser mParser;
  private final LineReader mIn;
  private final VcfHeader mHeader;
  private final int mNumSamples;
  private VcfRecord mCurrent;

  // Constructor for use by VcfReaderFactory
  VcfReader(VcfParser parser, BrLineReader in) throws IOException {
    this(parser, in, parser.parseHeader(in));
  }

  /**
   * Read VcfRecords from a region of a block-compressed file, pre-parsed header
   * @param parser used to parse each record line
   * @param reader source of record lines
   * @param header header for file currently being read (callers responsibility)
   * @throws IOException if an IO error occurs
   */
  VcfReader(VcfParser parser, LineReader reader, VcfHeader header) throws IOException {
    mParser = parser;
    mIn = reader;
    mHeader = header;
    mNumSamples = mHeader.getNumberOfSamples();
    setNext();
  }

  /**
   * Open a <code>VCF</code> reader from commonly used flag arguments
   * @param flags the flags parser with all arguments set
   * @return the reader
   * @throws IOException if an IO Error occurs
   */
  static VcfReader openVcfReader(CFlags flags) throws IOException {
    return new VcfReaderFactory(flags).make(flags);
  }

  /**
   * Open a <code>VCF</code> reader
   * @param f <code>VCF</code> file, optionally gzipped. If f is '-', input will be read from System.in instead
   * @return the reader
   * @throws IOException if an IO Error occurs
   */
  public static VcfReader openVcfReader(File f) throws IOException {
    return new VcfReaderFactory().make(f);
  }

  /**
   * Open a <code>VCF</code> reader, optionally with a region restriction
   * @param f <code>VCF</code> file, optionally gzipped. If f is '-', input will be read from System.in instead
   * @param ranges regions to restrict to, null if whole file should be used
   * @return the reader
   * @throws IOException if an IO Error occurs or if trying to apply a region restriction when reading from System.in
   */
  public static VcfReader openVcfReader(File f, ReferenceRanges<String> ranges) throws IOException {
    return new VcfReaderFactory().regions(ranges).make(f);
  }