package jalview.ext.htsjdk;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertTrue;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFFileReader;

import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.List;

import org.testng.annotations.Test;

public class VCFFileReaderTest
{
  private static final String[] VCF = new String[] {
      "##fileformat=VCFv4.2",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
      "20\t3\t.\tC\tG\t.\tPASS\tDP=100", // SNP C/G
      "20\t7\t.\tG\tGA\t.\tPASS\tDP=100", // insertion G/GA
      "18\t2\t.\tACG\tA\t.\tPASS\tDP=100" }; // deletion ACG/A

  /**
   * A test to exercise some basic functionality of the htsjdk VCF reader
   * 
   * @throws IOException
   */
  @Test(groups = "Functional")
  public void testReadVcf() throws IOException
  {
    File f = writeVcfFile();
    VCFFileReader reader = new VCFFileReader(f, false);
    CloseableIterator<VariantContext> variants = reader.iterator();

    /*
     * SNP C/G variant
     */
    VariantContext vc = variants.next();
    assertTrue(vc.isSNP());
    Allele ref = vc.getReference();
    assertEquals(ref.getBaseString(), "C");
    List<Allele> alleles = vc.getAlleles();
    assertEquals(alleles.size(), 2);
    assertTrue(alleles.get(0).isReference());
    assertEquals(alleles.get(0).getBaseString(), "C");
    assertFalse(alleles.get(1).isReference());
    assertEquals(alleles.get(1).getBaseString(), "G");

    /*
     * Insertion G -> GA
     */
    vc = variants.next();
    assertFalse(vc.isSNP());
    assertTrue(vc.isSimpleInsertion());
    ref = vc.getReference();
    assertEquals(ref.getBaseString(), "G");
    alleles = vc.getAlleles();
    assertEquals(alleles.size(), 2);
    assertTrue(alleles.get(0).isReference());
    assertEquals(alleles.get(0).getBaseString(), "G");
    assertFalse(alleles.get(1).isReference());
    assertEquals(alleles.get(1).getBaseString(), "GA");

    /*
     * Deletion ACG -> A
     */
    vc = variants.next();
    assertFalse(vc.isSNP());
    assertTrue(vc.isSimpleDeletion());
    ref = vc.getReference();
    assertEquals(ref.getBaseString(), "ACG");
    alleles = vc.getAlleles();
    assertEquals(alleles.size(), 2);
    assertTrue(alleles.get(0).isReference());
    assertEquals(alleles.get(0).getBaseString(), "ACG");
    assertFalse(alleles.get(1).isReference());
    assertEquals(alleles.get(1).getBaseString(), "A");

    assertFalse(variants.hasNext());

    variants.close();
    reader.close();
  }

  /**
   * Creates a temporary file to be read by the htsjdk VCF reader
   * 
   * @return
   * @throws IOException
   */
  protected File writeVcfFile() throws IOException
  {
    File f = File.createTempFile("Test", "vcf");
    f.deleteOnExit();
    PrintWriter pw = new PrintWriter(f);
    for (String vcfLine : VCF) {
      pw.println(vcfLine);
    }
    pw.close();
    return f;
  }
}