Class TabixLineReader

src/main/java/com/rtg/tabix/TabixLineReader.java:51–351

A class to wrap the Tabix line reading capability.

 * A class to wrap the Tabix line reading capability.
 */
public class TabixLineReader implements LineReader {

  private static LineReader getDelegate(File input, TabixIndexReader tir, RegionRestriction region) throws IOException {
    final LineReader reader;
    if (region == null) {
      reader = new SingleRestrictionLineReader(input, tir);
    } else {
      reader = new SingleRestrictionLineReader(input, tir, region);
    }
    return reader;
  }

  private static LineReader getDelegate(File input, TabixIndexReader tir, ReferenceRanges<String> ranges) throws IOException {
    final LineReader reader;
    if (ranges == null || ranges.allAvailable()) {
      reader = new SingleRestrictionLineReader(input, tir);
    } else {
      reader = new MultiRestrictionLineReader(input, tir, ranges);
    }
    return reader;
  }


  private final LineReader mDelegate;

  /**
   *
   * @param input input text file
   * @param tabix index for input file
   * @param region the region to extract, may be null for no restriction
   * @throws IOException if an IO error occurs
   */
  public TabixLineReader(File input, File tabix, RegionRestriction region) throws IOException {
    this(getDelegate(input, new TabixIndexReader(tabix), region));
  }

  /**
   *
   * @param input input text file
   * @param tabix index for input file
   * @param ranges the ranges to extract, may be null for no restrictions
   * @throws IOException if an IO error occurs
   */
  public TabixLineReader(File input, File tabix, ReferenceRanges<String> ranges) throws IOException {
    this(getDelegate(input, new TabixIndexReader(tabix), ranges));
  }

  /**
   * Used only by <code>VCFMerge</code>.
   * @param input input text file
   * @param tir tabix line reader
   * @param region the region restriction, may be null for no restriction
   * @throws IOException if an IO error occurs
   */
  public TabixLineReader(File input, TabixIndexReader tir, ReferenceRanges<String> region) throws IOException {
    this(getDelegate(input, tir, region));
  }