package jalview.ext.htsjdk;

import htsjdk.tribble.CloseableTribbleIterator;
import htsjdk.tribble.TabixFeatureReader;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFCodec;

import java.io.IOException;

import org.testng.annotations.Test;

public class TabixFeatureReaderTest
{
  // gnomAD exome variant dataset
  private static final String VCF_PATH = "/Volumes/gjb/smacgowan/NOBACK/resources/gnomad/gnomad.exomes.r2.0.1.sites.vcf.gz";

  // "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";

  /**
   * A 'test' that demonstrates querying an indexed VCF file for features in a
   * specified interval
   * 
   * @throws IOException
   */
  @Test
  public void testQuery() throws IOException
  {
    /*
     * if not specified, assumes index file is filename.tbi
     */
    TabixFeatureReader<VariantContext, VCFCodec> reader = new TabixFeatureReader<>(
            VCF_PATH, VCF_PATH, new VCFCodec());

    /*
     * gene NMT1 (human) is on chromosome 17
     * GCHR38 (Ensembl): 45051610-45109016
     * GCHR37 (gnoMAD): 43128978-43186384
     * CDS begins at offset 9720, first CDS variant at offset 9724
     */
    CloseableTribbleIterator<VariantContext> features = reader.query("17",
            43128978 + 9724, 43128978 + 9734); // first 11 CDS positions
    while (features.hasNext())
    {
      System.out.println(features.next().toString());
    }

    features.close();
    reader.close();
  }

}