package jalview.ext.htsjdk;

import htsjdk.samtools.util.CloseableIterator;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFFileReader;
import htsjdk.variant.vcf.VCFHeader;

import java.io.Closeable;
import java.io.File;
import java.io.IOException;

/**
 * A thin wrapper for htsjdk classes to read either plain, or compressed, or
 * compressed and indexed VCF files
 */
public class VCFReader implements Closeable, Iterable<VariantContext>
{
  private static final String GZ = "gz";

  private static final String TBI_EXTENSION = ".tbi";

  private boolean indexed;

  private VCFFileReader reader;

  /**
   * Constructor given a raw or compressed VCF file or a (tabix) index file
   * <p>
   * For now, file type is inferred from its suffix: .gz or .bgz for compressed
   * data, .tbi for an index file, anything else is assumed to be plain text
   * VCF.
   * 
   * @param f
   * @throws IOException
   */
  public VCFReader(String filePath) throws IOException
  {
    if (filePath.endsWith(GZ))
    {
      if (new File(filePath + TBI_EXTENSION).exists())
      {
        indexed = true;
      }
    }
    else if (filePath.endsWith(TBI_EXTENSION))
    {
      indexed = true;
      filePath = filePath.substring(0, filePath.length() - 4);
    }

    reader = new VCFFileReader(new File(filePath), indexed);
  }

  @Override
  public void close() throws IOException
  {
    if (reader != null)
    {
      reader.close();
    }
  }

  /**
   * Returns an iterator over VCF variants in the file. The client should call
   * close() on the iterator when finished with it.
   */
  @Override
  public CloseableIterator<VariantContext> iterator()
  {
    return reader == null ? null : reader.iterator();
  }

  /**
   * Queries for records overlapping the region specified. Note that this method
   * requires a VCF file with an associated index. If no index exists a
   * TribbleException will be thrown. Client code should call close() on the
   * iterator when finished with it.
   * 
   * @param chrom
   *          the chromosome to query
   * @param start
   *          query interval start
   * @param end
   *          query interval end
   * @return
   */
  public CloseableIterator<VariantContext> query(final String chrom,
          final int start, final int end)
  {
    return reader == null ? null : reader.query(chrom, start, end);
  }

  /**
   * Returns an object that models the VCF file headers
   * 
   * @return
   */
  public VCFHeader getFileHeader()
  {
    return reader == null ? null : reader.getFileHeader();
  }
}